Question: FeatureExpressionSet using list.files() in place of read.xysfiles()
0
gravatar for Johnson, Franklin Theodore
6.4 years ago by
Dear Dr. Carvalho, Thanks for the reply. I saw the thread of FAQs how to read in the annotation package made using pdInfoBuilder. For anyone having issues, it seems as straight forward as: #install pdinfo.gpl11164.ndf.txt install.packages("pd.pdinfo.gpl11164.ndf.txt", type="source", repos=NULL) Installing package into ?C:/Users/ZHUGRP/Documents/R/win-library/3.0? (as ?lib? is unspecified) * installing *source* package 'pd.pdinfo.gpl11164.ndf.txt' ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded *** arch - i386 *** arch - x64 * DONE (pd.pdinfo.gpl11164.ndf.txt) ###################################################################### ###################################### I am currently trying to make the FeatureExpressionSet with my converted PAIR -> XYS.txt files unfortunately obtaining X/Y/S only. NimbleScan expected .tiff files to read into the software. These files were not available from NCBI/GEO. NimbleGen also did not respond to my inquiry regarding this matter to be able to obtain XYS files from available PAIR files. Using R, I'm testing 12 of 24 tab-delimited XYS files, to also test the annotation package made using pdInfoBuilder. #read in files from wd() filelist=list.files(pattern=".*.txt") > filelist [1] "GSM01.txt" "GSM02.txt" "GSM03.txt" "GSM04.txt" "GSM05.txt" "GSM06.txt" "GSM07.txt" "GSM08.txt" "GSM09.txt" "GSM10.txt" "GSM11.txt" "GSM12.txt" #read in each data file in filelist as a matrix to make EFS object > datalist=lapply(filelist, function(x)as.matrix(read.table(x, header=T, sep="\t", as.is=T))) #construct phenoData frame > theData=data.frame(Key=rep(c("Week0","Week-2","Week-4"), each=4)) > rownames(theData)=basename(filelist) > pd=new("AnnotatedDataFrame", data=theData) .... However, I fail the EFS construction: hardline=new("ExpressionFeatureSet", datalist, phenoData=pd, annotation=library(pd.pdinfo.gpl11164.ndf.txt)) Error in .names_found_unique(names(value), names(object)) : 'sampleNames' replacement list must have unique named elements corresponding to assayData element names To confirm, > sampleNames(datalist) [1] "X" "Y" "PM" So, it seems EFS is expecting unique sampleNames for each file in filelist? How to read in multiple files into an efs object, as is done with read.xysfiles? Is this doable? Is it necessary to execute datalist=lapply(filelist, function(x)as.matrix(read.table(x, header=T, sep="\t", as.is=T))) surrounded with Booleans to make the object TRUE, per se? i.e. (datalist=lapply(filelist, function(x)as.matrix(read.table(x, header=T, sep="\t", as.is=T))) ) Best Regards, Franklin Great minds discuss ideas. Average minds discuss events. Small minds discuss people. -Eleanor Roosevelt ________________________________________ From: Benilton Carvalho [beniltoncarvalho@gmail.com] Sent: Thursday, June 13, 2013 4:43 PM To: Johnson, Franklin Theodore Cc: bioconductor at r-project.org Subject: Re: [BioC] PAIR files -- feature set table dont worry about that particular warning.... just install the package and try to read your XYS files. 2013/6/13 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: > Dr. Carvalho, > > Yes. I see what you mean. > Switching the columns helped in the FeatureSet table loading inserted more > that 2 rows: > > Inserting 198661 rows into table featureSet... OK > However, the warning message did print again. > > > Warning message: > In is.na(ndfdata[["SIGNAL"]]) : > is.na() applied to non-(list or vector) of type 'NULL' > > Below is the output + sessionInfo(), as I upgraded to R 3.0.1. > > #Begin R command line code: > >> makePdInfoPackage(arrays, destDir = getwd(), unlink=TRUE) > ==================================================================== ====================================================================== ==================== > > > Building annotation package for Nimblegen Expression Array > NDF: pdinfo_GPL11164.ndf.txt <-new .ndf file with PROBE_ID<->SEQ_ID > XYS: XYS.txt > ==================================================================== ====================================================================== ==================== > Parsing file: pdinfo_GPL11164.ndf.txt... OK > > Parsing file: XYS.txt... OK > Merging NDF and XYS files... OK > Preparing contents for featureSet table... OK > Preparing contents for bgfeature table... OK > Preparing contents for pmfeature table... OK > Creating package in E:/RANDOM/Test/Yanmin's Microarray Paper/Yanmin > Microarray RAW/pd.pdinfo.gpl11164.ndf.txt > Inserting 198661 rows into table featureSet... OK > Inserting 770599 rows into table pmfeature... OK > > Counting rows in featureSet > Counting rows in pmfeature > Creating index idx_pmfsetid on pmfeature... OK > Creating index idx_pmfid on pmfeature... OK > Creating index idx_fsfsetid on featureSet... OK > Saving DataFrame object for PM. > Done. > Warning message: > In is.na(ndfdata[["SIGNAL"]]) : > is.na() applied to non-(list or vector) of type 'NULL' > > >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: i386-w64-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > States.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] pdInfoBuilder_1.24.0 oligo_1.24.0 oligoClasses_1.22.0 > affxparser_1.32.1 RSQLite_0.11.4 DBI_0.2-7 > Biobase_2.20.0 > [8] BiocGenerics_0.6.0 BiocInstaller_1.10.2 > > loaded via a namespace (and not attached): > [1] affyio_1.28.0 Biostrings_2.28.0 bit_1.1-10 > codetools_0.2-8 ff_2.2-11 foreach_1.4.1 > GenomicRanges_1.12.4 > [8] IRanges_1.18.1 iterators_1.0.6 preprocessCore_1.22.0 > splines_3.0.1 stats4_3.0.1 tools_3.0.1 > zlibbioc_1.6.0 > > > >>q() > > > > The built pdInfopackage loaded in Destdir is identical to previous message. > > However the featureSet table now has more than 2 rows... > > Lastly, I did multiple combos, as my merged file has (X.x, Y.x)<-seems to be > identifiers for the 'probe IDs' on the array as well as (X.y, Y.y) <- seems > to be the sequence identifiers for the "SEQ_ID". I used X.x, Y.x and PM > which gave the result I pasted above. All others had errors. I'm close, but > that Warning Message is annoying... > > > > Regards, > > Franklin > > > Great minds discuss ideas. Average minds discuss events. Small minds discuss > people. -Eleanor Roosevelt > > > > > ________________________________________ > From: Benilton Carvalho [beniltoncarvalho at gmail.com] > Sent: Wednesday, June 12, 2013 8:25 PM > > To: Johnson, Franklin Theodore > Cc: bioconductor at r-project.org > Subject: Re: [BioC] PAIR files -- feature set table > > That does not look ok. > > The problem is the count for the featureSet table... This table stores > the information for "genes" (or whatever the target for this > particular array is)... so, it is unlikely that you have a microarray > with only 2 "target units"... I'd expect something around the > thousands... > > pdInfoBuilder uses the information in SEQ_ID (in the NDF) to get the > target information (i.e., the contents for featureSet). > > Given that this is a custom array, I believe that the best idea is to > contact the person who designed it and ask more details about the > design (in particular, how many probesets and average number of probes > per probeset)... > > I've seen some designs in which the information that was expected to > be in SEQ_ID was actually stored in PROBE_ID (in such cases, the user > needs to create a backup copy of the NDF, and then move the contents > of PROBE_ID to SEQ_ID - and vice-versa). > > b > > 2013/6/12 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: >> Dear Dr. Carvalho, >> >> Recently, we had cooresponence regaring makePDInfoPackage for an NimbleGen >> apple microarray. >> I was able to merge the ndf design and XYS files using PROBE_ID. >> As a reminder this is a custom array, and there are no SIGNAL==NAs for >> control probes. >> It seemed to work: >>> makePdInfoPackage(seed, destDir("")) >> >> =================================================================== ====================================================================== =================== >> Building annotation package for Nimblegen Expression Array >> NDF: GPL11164.ndf >> XYS: XYS.txt >> >> =================================================================== ====================================================================== =================== >> Parsing file: GPL11164.ndf... OK >> Parsing file: XYS.txt... OK >> Merging NDF and XYS files... OK >> Preparing contents for featureSet table... OK >> Preparing contents for bgfeature table... OK >> Preparing contents for pmfeature table... OK >> Creating package in >> C:/Users/franklin.johnson.PW50-WEN/Desktop/Test/Yanmin's Microarray >> Paper/Yanmin Microarray RAW/pd.gpl11164 >> Inserting 2 rows into table featureSet... OK >> Inserting 765524 rows into table pmfeature... OK >> Inserting 5075 rows into table bgfeature... OK >> Counting rows in bgfeature >> Counting rows in featureSet >> Counting rows in pmfeature >> Creating index idx_bgfsetid on bgfeature... OK >> Creating index idx_bgfid on bgfeature... OK >> Creating index idx_pmfsetid on pmfeature... OK >> Creating index idx_pmfid on pmfeature... OK >> Creating index idx_fsfsetid on featureSet... OK >> Saving DataFrame object for PM. >> Saving DataFrame object for BG. >> Done. >> Warning message: >> In is.na(ndfdata[["SIGNAL"]]) : >> is.na() applied to non-(list or vector) of type 'NULL' >>> >> >> In contrast to this warning message, I see a pdinfopackage directory with >> 4 subdirectories: c=("data", "inst", "man", R"), as well as >> subsubdirectories in "inst"=c("extdata", and "Unit Tests"), in addition to >> two text files in the main directory: c=("DESCRIPTION", "NAMESPACE") were >> created in my destination folder. >> Before using "oligo", if possible, I wanted to confirm with you that this >> package is viable to use with "oligo" although a warning message that may >> not pertain to my custom designed microarray was printed. >> >> Regards, >> Franklin >> >> Great minds discuss ideas. Average minds discuss events. Small minds >> discuss people. -Eleanor Roosevelt >> >> >> >> >> ________________________________________ >> From: Johnson, Franklin Theodore >> Sent: Friday, June 07, 2013 10:39 AM >> To: Benilton Carvalho >> Cc: bioconductor at r-project.org >> Subject: RE: [BioC] PAIR files -- feature set table >> >> Resending to bioconductor message thread: >> >> Dear Dr. Carvalho, >> Thanks for the response. >> As you suggested, I will look into the merge function using "Probe_ID". >> After reading in the data, I will start here: merge.datasets(dataset1, >> dataset2, by="key"). >> Best Regards, >> Franklin >> >> Great minds discuss ideas. Average minds discuss events. Small minds >> discuss people. -Eleanor Roosevelt >> >> ________________________________________ >> From: Benilton Carvalho [beniltoncarvalho at gmail.com] >> Sent: Thursday, June 06, 2013 8:11 PM >> To: Johnson, Franklin Theodore >> Cc: bioconductor at r-project.org; franklin.johnson at wsu.edu >> Subject: Re: [BioC] PAIR files -- feature set table >> >> You will need to merge the PAIR and the NDF using the PROBE_ID column >> as key. This will allow you to get the X/Y coordinates needed to >> create the XYS as described on the other messages. >> >> Regarding annotation, you may need to contact NimbleGen to request >> this information directly from them... >> >> benilton >> >> 2013/6/6 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: >>> Dear Dr. Carvalho, >>> >>> Muchos grasias for the reply. >>> >>> Actually, this is what my .ndf file looks like: >>>> head(ndf) >>> PROBE_DESIGN_ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA SEQ_ID >>> 1 7552_0343_0009 Duplicate_1 >>> 2 7552_0345_0009 Duplicate_2 >>> 3 7552_0347_0009 Duplicate_1 >>> 4 7552_0349_0009 Duplicate_2 >>> 5 7552_0351_0009 Duplicate_2 >>> 6 7552_0353_0009 Duplicate_1 >>> PROBE_SEQUENCE MISMATCH >>> MATCH_INDEX FEATURE_ID ROW_NUM COL_NUM PROBE_CLASS >>> 1 cttgactcttctaagttcaaaggtaactcaagtgaagctgtcagatatgatccttcca 0 >>> 64535488 64535488 9 343 >>> 2 cccaagcattaaaccttactcatatacttataatgcagccatcaagagtttgtgcaagg 0 >>> 64799310 64799310 9 345 >>> 3 agggaggctgaaagagagagtgaatggtccagctgggcataattgctgca 0 >>> 64476989 64476989 9 347 >>> 4 ttgttggtgggggtgttgcccttagtaccccagaccttgaagcagttaaa 0 >>> 64862794 64862794 9 349 >>> 5 gtgtggggccccctttctttaactggaacctttctttgaagcaatttggg 0 >>> 64832726 64832726 9 351 >>> 6 ttgtccaattccaacatgccgagacggcagggattgtgatcgtgttgttc 0 >>> 64435686 64435686 9 353 >>> PROBE_ID POSITION DESIGN_ID X Y >>> 1 Contig19819_1_f_28_10_535 0 7552 343 9 >>> 2 Malus_CN899188_2_f_147_1_755 0 7552 345 9 >>> 3 Contig20738_8_r_1179_2_1432 0 7552 347 9 >>> 4 Malus_CN880097_2_r_336_2_536 0 7552 349 9 >>> 5 Malus_CN918117_2_f_632_1_781 0 7552 351 9 >>> 6 Contig1991_1_f_71_2_1239 0 7552 353 9 >>> >>> The pair files, .532 pair files only (one-color arrays), only obtain the >>> probe ID and signal; after some text at the top describing the experiment. >>> My real issue is that I can further normalize and analyze the RMA files with >>> sva and limma, etc. However, I cannot annotate the probes without the array >>> annotation, as there are duplicates in the ndf file which are removed in the >>> RMA.pair files available on NCBI/GEO. So they will not match in any >>> annotation package I've failed at trying. >>> So, I' tried to go back and start from the raw pair files...this custom >>> array is really a "custom" array without >>> NimbleScan. >>> >>> Salud, >>> Franklin >>> >>> >>> >>> >>> >>> >>> Great minds discuss ideas. Average minds discuss events. Small minds >>> discuss people. -Eleanor Roosevelt >>> >>> >>> >>> >>> ________________________________________ >>> From: Benilton Carvalho [beniltoncarvalho at gmail.com] >>> Sent: Wednesday, June 05, 2013 6:42 PM >>> To: FRANKLIN JOHNSON [guest] >>> Cc: bioconductor at r-project.org; franklin.johnson at wsu.edu; pdInfoBuilder >>> Maintainer >>> Subject: Re: [BioC] PAIR files -- feature set table >>> >>> It's an unfortunate mistake to have the pairFile *argument* in the >>> call (not in the slots session, but I see your point). :-( I'll make >>> sure that this is fixed. >>> >>> You need to convert the PAIR files to XYS... >>> >>> Some refs that should help you in the process: >>> >>> https://stat.ethz.ch/pipermail/bioconductor/2012-January/043186.html >>> >>> http://comments.gmane.org/gmane.science.biology.informatics.conduc tor/27547 >>> >>> b >>> >>> 2013/6/5 FRANKLIN JOHNSON [guest] <guest at="" bioconductor.org="">: >>>> >>>> Dear Maintainer, >>>> >>>> I downloaded available NimbleGen 'single channel' 532.PAIR files for a >>>> custom built expression microarray from NCBI/GEO (GPL11164). However, I get >>>> an error message when I try to make the annotation for this platform using >>>> pdInfoBuild. >>>> >>>> In pdInfoBuilder Reference Manual (June 5, 2013), under the >>>> NgsExpressionPDInfoPkgSeed method, there is a slot for pairFile, although, >>>> showClasses("Ngs.."), does not show a slot for this, only, XYS. Thus, I >>>> changed the .pair file extension to .xys. >>>> >>>> (ndf<- list.files(getwd(), pattern=".ndf", full.names=TRUE)) # read >>>> annotation file >>>> [1] "C:/Users/franklin.johnson.PW99-WEN/Desktop/Test/Yanmin's Microarray >>>> Paper/Yanmin Microarray RAW/GPL11164.ndf" >>>> >>>> (xys <- list.files(getwd(), pattern = ".xys", full.names = TRUE)[1]) >>>> [1] "C:/Users/franklin.johnson.PW99-WEN/Desktop/Test/Yanmin's Microarray >>>> Paper/Yanmin Microarray RAW/GSM618107_14418002_532.xys" >>>> >>>> But, doing this resulted in an error message: >>>> seed <- new("NgsExpressionPDInfoPkgSeed", ndfFile = ndf, xysFile = xys, >>>> author = "FJ", organism = "Apple", species = "Malus x Domestica cv.GD") >>>> >>>> makePdInfoPackage(arrays, destDir = getwd()) >>>> >>>> ================================================================= ====================================================================== ===== >>>> Building annotation package for Nimblegen Expression Array >>>> NDF: GPL11164.ndf >>>> XYS: GSM618107_14418002_532.xys >>>> >>>> ================================================================= ====================================================================== ===== >>>> Parsing file: GPL11164.ndf... OK >>>> Parsing file: GSM618107_14418002_532.xys... OK >>>> Merging NDF and XYS files... OK >>>> Preparing contents for featureSet table... Error in >>>> `[.data.frame`(ndfdata, , colsFS) : undefined columns selected >>>> In addition: Warning message: >>>> In is.na(ndfdata[["SIGNAL"]]) : >>>> is.na() applied to non-(list or vector) of type 'NULL' >>>> >>>> The only files available from NCBI/GEO are 24 PAIR files and 1 ndf. It >>>> seems .xys has a different arrangement than .pair, thus .ndf is not >>>> applicable to annotate the .pair file? Any suggestions? >>>> Hope to hear from you soon. >>>> Franklin >>>> >>>> -- output of sessionInfo(): >>>> >>>>> sessionInfo() >>>> R version 3.0.1 (2013-05-16) >>>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>>> >>>> locale: >>>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >>>> States.1252 LC_MONETARY=English_United States.1252 >>>> [4] LC_NUMERIC=C LC_TIME=English_United >>>> States.1252 >>>> >>>> attached base packages: >>>> [1] tcltk grid parallel stats graphics grDevices utils >>>> datasets methods base >>>> >>>> other attached packages: >>>> [1] pdInfoBuilder_1.24.0 oligo_1.24.0 oligoClasses_1.22.0 >>>> affxparser_1.32.1 RSQLite_0.11.4 DBI_0.2-7 >>>> [7] Mfuzz_2.18.0 DynDoc_1.38.0 widgetTools_1.38.0 >>>> e1071_1.6-1 class_7.3-7 gplots_2.11.0.1 >>>> [13] KernSmooth_2.23-10 caTools_1.14 gdata_2.12.0.2 >>>> gtools_2.7.1 timecourse_1.32.0 MASS_7.3-26 >>>> [19] Biobase_2.20.0 BiocGenerics_0.6.0 limma_3.16.5 >>>> ggplot2_0.9.3.1 BiocInstaller_1.10.1 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] affyio_1.28.0 Biostrings_2.28.0 bit_1.1-10 >>>> bitops_1.0-5 codetools_0.2-8 colorspace_1.2-2 >>>> [7] dichromat_2.0-0 digest_0.6.3 ff_2.2-11 >>>> foreach_1.4.0 GenomicRanges_1.12.4 gtable_0.1.2 >>>> [13] IRanges_1.18.1 iterators_1.0.6 labeling_0.1 >>>> marray_1.38.0 munsell_0.4 plyr_1.8 >>>> [19] preprocessCore_1.22.0 proto_0.3-10 RColorBrewer_1.0-5 >>>> reshape2_1.2.2 scales_0.2.3 splines_3.0.1 >>>> [25] stats4_3.0.1 stringr_0.6.2 tkWidgets_1.38.0 >>>> tools_3.0.1 zlibbioc_1.6.0 >>>>> >>>> >>>> >>>> -- >>>> Sent via the guest posting facility at bioconductor.org. >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>
ADD COMMENTlink modified 6.4 years ago by Benilton Carvalho4.3k • written 6.4 years ago by Johnson, Franklin Theodore140
Answer: FeatureExpressionSet using list.files() in place of read.xysfiles()
0
gravatar for Benilton Carvalho
6.4 years ago by
Brazil/Campinas/UNICAMP
Benilton Carvalho4.3k wrote:
Dear Franklin, I'm not sure I follow your message... my most sincere apologies... Now that you have your XYS files, I was expecting you to simply use: library(oligo) rawData = read.xysfiles(filelist, pkgname='pd.pdinfo.gpl11164.ndf.txt') doesn't this work for you? (the 'filelist' variable above contains the names of your converted XYS files) Let me know what are your findings... b 2013/6/19 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: > Dear Dr. Carvalho, > > Thanks for the reply. > I saw the thread of FAQs how to read in the annotation package made using pdInfoBuilder. > For anyone having issues, it seems as straight forward as: > #install pdinfo.gpl11164.ndf.txt > install.packages("pd.pdinfo.gpl11164.ndf.txt", type="source", repos=NULL) > Installing package into ?C:/Users/ZHUGRP/Documents/R/win- library/3.0? > (as ?lib? is unspecified) > * installing *source* package 'pd.pdinfo.gpl11164.ndf.txt' ... > ** R > ** data > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices > ** testing if installed package can be loaded > *** arch - i386 > *** arch - x64 > * DONE (pd.pdinfo.gpl11164.ndf.txt) > #################################################################### ######################################## > I am currently trying to make the FeatureExpressionSet with my converted PAIR -> XYS.txt files unfortunately obtaining X/Y/S only. > NimbleScan expected .tiff files to read into the software. These files were not available from NCBI/GEO. NimbleGen also did not respond to my inquiry regarding this matter to be able to obtain XYS files from available PAIR files. Using R, I'm testing 12 of 24 tab-delimited XYS files, to also test the annotation package made using pdInfoBuilder. > #read in files from wd() > filelist=list.files(pattern=".*.txt") >> filelist > [1] "GSM01.txt" "GSM02.txt" "GSM03.txt" "GSM04.txt" "GSM05.txt" "GSM06.txt" "GSM07.txt" "GSM08.txt" "GSM09.txt" "GSM10.txt" "GSM11.txt" "GSM12.txt" > #read in each data file in filelist as a matrix to make EFS object >> datalist=lapply(filelist, function(x)as.matrix(read.table(x, header=T, sep="\t", as.is=T))) > #construct phenoData frame >> theData=data.frame(Key=rep(c("Week0","Week-2","Week-4"), each=4)) >> rownames(theData)=basename(filelist) >> pd=new("AnnotatedDataFrame", data=theData) > .... > However, I fail the EFS construction: > hardline=new("ExpressionFeatureSet", datalist, phenoData=pd, annotation=library(pd.pdinfo.gpl11164.ndf.txt)) > Error in .names_found_unique(names(value), names(object)) : > 'sampleNames' replacement list must have unique named elements corresponding to assayData element names > To confirm, >> sampleNames(datalist) > [1] "X" "Y" "PM" > So, it seems EFS is expecting unique sampleNames for each file in filelist? > How to read in multiple files into an efs object, as is done with read.xysfiles? Is this doable? > > Is it necessary to execute datalist=lapply(filelist, function(x)as.matrix(read.table(x, header=T, sep="\t", as.is=T))) surrounded with Booleans to make the object TRUE, per se? > i.e. (datalist=lapply(filelist, function(x)as.matrix(read.table(x, header=T, sep="\t", as.is=T))) ) > Best Regards, > Franklin > > Great minds discuss ideas. Average minds discuss events. Small minds discuss people. -Eleanor Roosevelt > > > > > ________________________________________ > From: Benilton Carvalho [beniltoncarvalho at gmail.com] > Sent: Thursday, June 13, 2013 4:43 PM > To: Johnson, Franklin Theodore > Cc: bioconductor at r-project.org > Subject: Re: [BioC] PAIR files -- feature set table > > dont worry about that particular warning.... just install the package > and try to read your XYS files. > > 2013/6/13 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: >> Dr. Carvalho, >> >> Yes. I see what you mean. >> Switching the columns helped in the FeatureSet table loading inserted more >> that 2 rows: >> >> Inserting 198661 rows into table featureSet... OK >> However, the warning message did print again. >> >> >> Warning message: >> In is.na(ndfdata[["SIGNAL"]]) : >> is.na() applied to non-(list or vector) of type 'NULL' >> >> Below is the output + sessionInfo(), as I upgraded to R 3.0.1. >> >> #Begin R command line code: >> >>> makePdInfoPackage(arrays, destDir = getwd(), unlink=TRUE) >> =================================================================== ====================================================================== ===================== >> >> >> Building annotation package for Nimblegen Expression Array >> NDF: pdinfo_GPL11164.ndf.txt <-new .ndf file with PROBE_ID<->SEQ_ID >> XYS: XYS.txt >> =================================================================== ====================================================================== ===================== >> Parsing file: pdinfo_GPL11164.ndf.txt... OK >> >> Parsing file: XYS.txt... OK >> Merging NDF and XYS files... OK >> Preparing contents for featureSet table... OK >> Preparing contents for bgfeature table... OK >> Preparing contents for pmfeature table... OK >> Creating package in E:/RANDOM/Test/Yanmin's Microarray Paper/Yanmin >> Microarray RAW/pd.pdinfo.gpl11164.ndf.txt >> Inserting 198661 rows into table featureSet... OK >> Inserting 770599 rows into table pmfeature... OK >> >> Counting rows in featureSet >> Counting rows in pmfeature >> Creating index idx_pmfsetid on pmfeature... OK >> Creating index idx_pmfid on pmfeature... OK >> Creating index idx_fsfsetid on featureSet... OK >> Saving DataFrame object for PM. >> Done. >> Warning message: >> In is.na(ndfdata[["SIGNAL"]]) : >> is.na() applied to non-(list or vector) of type 'NULL' >> >> >>> sessionInfo() >> R version 3.0.1 (2013-05-16) >> Platform: i386-w64-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> States.1252 LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C LC_TIME=English_United >> States.1252 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] pdInfoBuilder_1.24.0 oligo_1.24.0 oligoClasses_1.22.0 >> affxparser_1.32.1 RSQLite_0.11.4 DBI_0.2-7 >> Biobase_2.20.0 >> [8] BiocGenerics_0.6.0 BiocInstaller_1.10.2 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.28.0 Biostrings_2.28.0 bit_1.1-10 >> codetools_0.2-8 ff_2.2-11 foreach_1.4.1 >> GenomicRanges_1.12.4 >> [8] IRanges_1.18.1 iterators_1.0.6 preprocessCore_1.22.0 >> splines_3.0.1 stats4_3.0.1 tools_3.0.1 >> zlibbioc_1.6.0 >> >> >> >>>q() >> >> >> >> The built pdInfopackage loaded in Destdir is identical to previous message. >> >> However the featureSet table now has more than 2 rows... >> >> Lastly, I did multiple combos, as my merged file has (X.x, Y.x)<-seems to be >> identifiers for the 'probe IDs' on the array as well as (X.y, Y.y) <- seems >> to be the sequence identifiers for the "SEQ_ID". I used X.x, Y.x and PM >> which gave the result I pasted above. All others had errors. I'm close, but >> that Warning Message is annoying... >> >> >> >> Regards, >> >> Franklin >> >> >> Great minds discuss ideas. Average minds discuss events. Small minds discuss >> people. -Eleanor Roosevelt >> >> >> >> >> ________________________________________ >> From: Benilton Carvalho [beniltoncarvalho at gmail.com] >> Sent: Wednesday, June 12, 2013 8:25 PM >> >> To: Johnson, Franklin Theodore >> Cc: bioconductor at r-project.org >> Subject: Re: [BioC] PAIR files -- feature set table >> >> That does not look ok. >> >> The problem is the count for the featureSet table... This table stores >> the information for "genes" (or whatever the target for this >> particular array is)... so, it is unlikely that you have a microarray >> with only 2 "target units"... I'd expect something around the >> thousands... >> >> pdInfoBuilder uses the information in SEQ_ID (in the NDF) to get the >> target information (i.e., the contents for featureSet). >> >> Given that this is a custom array, I believe that the best idea is to >> contact the person who designed it and ask more details about the >> design (in particular, how many probesets and average number of probes >> per probeset)... >> >> I've seen some designs in which the information that was expected to >> be in SEQ_ID was actually stored in PROBE_ID (in such cases, the user >> needs to create a backup copy of the NDF, and then move the contents >> of PROBE_ID to SEQ_ID - and vice-versa). >> >> b >> >> 2013/6/12 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: >>> Dear Dr. Carvalho, >>> >>> Recently, we had cooresponence regaring makePDInfoPackage for an NimbleGen >>> apple microarray. >>> I was able to merge the ndf design and XYS files using PROBE_ID. >>> As a reminder this is a custom array, and there are no SIGNAL==NAs for >>> control probes. >>> It seemed to work: >>>> makePdInfoPackage(seed, destDir("")) >>> >>> ================================================================== ====================================================================== ==================== >>> Building annotation package for Nimblegen Expression Array >>> NDF: GPL11164.ndf >>> XYS: XYS.txt >>> >>> ================================================================== ====================================================================== ==================== >>> Parsing file: GPL11164.ndf... OK >>> Parsing file: XYS.txt... OK >>> Merging NDF and XYS files... OK >>> Preparing contents for featureSet table... OK >>> Preparing contents for bgfeature table... OK >>> Preparing contents for pmfeature table... OK >>> Creating package in >>> C:/Users/franklin.johnson.PW50-WEN/Desktop/Test/Yanmin's Microarray >>> Paper/Yanmin Microarray RAW/pd.gpl11164 >>> Inserting 2 rows into table featureSet... OK >>> Inserting 765524 rows into table pmfeature... OK >>> Inserting 5075 rows into table bgfeature... OK >>> Counting rows in bgfeature >>> Counting rows in featureSet >>> Counting rows in pmfeature >>> Creating index idx_bgfsetid on bgfeature... OK >>> Creating index idx_bgfid on bgfeature... OK >>> Creating index idx_pmfsetid on pmfeature... OK >>> Creating index idx_pmfid on pmfeature... OK >>> Creating index idx_fsfsetid on featureSet... OK >>> Saving DataFrame object for PM. >>> Saving DataFrame object for BG. >>> Done. >>> Warning message: >>> In is.na(ndfdata[["SIGNAL"]]) : >>> is.na() applied to non-(list or vector) of type 'NULL' >>>> >>> >>> In contrast to this warning message, I see a pdinfopackage directory with >>> 4 subdirectories: c=("data", "inst", "man", R"), as well as >>> subsubdirectories in "inst"=c("extdata", and "Unit Tests"), in addition to >>> two text files in the main directory: c=("DESCRIPTION", "NAMESPACE") were >>> created in my destination folder. >>> Before using "oligo", if possible, I wanted to confirm with you that this >>> package is viable to use with "oligo" although a warning message that may >>> not pertain to my custom designed microarray was printed. >>> >>> Regards, >>> Franklin >>> >>> Great minds discuss ideas. Average minds discuss events. Small minds >>> discuss people. -Eleanor Roosevelt >>> >>> >>> >>> >>> ________________________________________ >>> From: Johnson, Franklin Theodore >>> Sent: Friday, June 07, 2013 10:39 AM >>> To: Benilton Carvalho >>> Cc: bioconductor at r-project.org >>> Subject: RE: [BioC] PAIR files -- feature set table >>> >>> Resending to bioconductor message thread: >>> >>> Dear Dr. Carvalho, >>> Thanks for the response. >>> As you suggested, I will look into the merge function using "Probe_ID". >>> After reading in the data, I will start here: merge.datasets(dataset1, >>> dataset2, by="key"). >>> Best Regards, >>> Franklin >>> >>> Great minds discuss ideas. Average minds discuss events. Small minds >>> discuss people. -Eleanor Roosevelt >>> >>> ________________________________________ >>> From: Benilton Carvalho [beniltoncarvalho at gmail.com] >>> Sent: Thursday, June 06, 2013 8:11 PM >>> To: Johnson, Franklin Theodore >>> Cc: bioconductor at r-project.org; franklin.johnson at wsu.edu >>> Subject: Re: [BioC] PAIR files -- feature set table >>> >>> You will need to merge the PAIR and the NDF using the PROBE_ID column >>> as key. This will allow you to get the X/Y coordinates needed to >>> create the XYS as described on the other messages. >>> >>> Regarding annotation, you may need to contact NimbleGen to request >>> this information directly from them... >>> >>> benilton >>> >>> 2013/6/6 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: >>>> Dear Dr. Carvalho, >>>> >>>> Muchos grasias for the reply. >>>> >>>> Actually, this is what my .ndf file looks like: >>>>> head(ndf) >>>> PROBE_DESIGN_ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA SEQ_ID >>>> 1 7552_0343_0009 Duplicate_1 >>>> 2 7552_0345_0009 Duplicate_2 >>>> 3 7552_0347_0009 Duplicate_1 >>>> 4 7552_0349_0009 Duplicate_2 >>>> 5 7552_0351_0009 Duplicate_2 >>>> 6 7552_0353_0009 Duplicate_1 >>>> PROBE_SEQUENCE MISMATCH >>>> MATCH_INDEX FEATURE_ID ROW_NUM COL_NUM PROBE_CLASS >>>> 1 cttgactcttctaagttcaaaggtaactcaagtgaagctgtcagatatgatccttcca 0 >>>> 64535488 64535488 9 343 >>>> 2 cccaagcattaaaccttactcatatacttataatgcagccatcaagagtttgtgcaagg 0 >>>> 64799310 64799310 9 345 >>>> 3 agggaggctgaaagagagagtgaatggtccagctgggcataattgctgca 0 >>>> 64476989 64476989 9 347 >>>> 4 ttgttggtgggggtgttgcccttagtaccccagaccttgaagcagttaaa 0 >>>> 64862794 64862794 9 349 >>>> 5 gtgtggggccccctttctttaactggaacctttctttgaagcaatttggg 0 >>>> 64832726 64832726 9 351 >>>> 6 ttgtccaattccaacatgccgagacggcagggattgtgatcgtgttgttc 0 >>>> 64435686 64435686 9 353 >>>> PROBE_ID POSITION DESIGN_ID X Y >>>> 1 Contig19819_1_f_28_10_535 0 7552 343 9 >>>> 2 Malus_CN899188_2_f_147_1_755 0 7552 345 9 >>>> 3 Contig20738_8_r_1179_2_1432 0 7552 347 9 >>>> 4 Malus_CN880097_2_r_336_2_536 0 7552 349 9 >>>> 5 Malus_CN918117_2_f_632_1_781 0 7552 351 9 >>>> 6 Contig1991_1_f_71_2_1239 0 7552 353 9 >>>> >>>> The pair files, .532 pair files only (one-color arrays), only obtain the >>>> probe ID and signal; after some text at the top describing the experiment. >>>> My real issue is that I can further normalize and analyze the RMA files with >>>> sva and limma, etc. However, I cannot annotate the probes without the array >>>> annotation, as there are duplicates in the ndf file which are removed in the >>>> RMA.pair files available on NCBI/GEO. So they will not match in any >>>> annotation package I've failed at trying. >>>> So, I' tried to go back and start from the raw pair files...this custom >>>> array is really a "custom" array without >>>> NimbleScan. >>>> >>>> Salud, >>>> Franklin >>>> >>>> >>>> >>>> >>>> >>>> >>>> Great minds discuss ideas. Average minds discuss events. Small minds >>>> discuss people. -Eleanor Roosevelt >>>> >>>> >>>> >>>> >>>> ________________________________________ >>>> From: Benilton Carvalho [beniltoncarvalho at gmail.com] >>>> Sent: Wednesday, June 05, 2013 6:42 PM >>>> To: FRANKLIN JOHNSON [guest] >>>> Cc: bioconductor at r-project.org; franklin.johnson at wsu.edu; pdInfoBuilder >>>> Maintainer >>>> Subject: Re: [BioC] PAIR files -- feature set table >>>> >>>> It's an unfortunate mistake to have the pairFile *argument* in the >>>> call (not in the slots session, but I see your point). :-( I'll make >>>> sure that this is fixed. >>>> >>>> You need to convert the PAIR files to XYS... >>>> >>>> Some refs that should help you in the process: >>>> >>>> https://stat.ethz.ch/pipermail/bioconductor/2012-January/043186.html >>>> >>>> http://comments.gmane.org/gmane.science.biology.informatics.condu ctor/27547 >>>> >>>> b >>>> >>>> 2013/6/5 FRANKLIN JOHNSON [guest] <guest at="" bioconductor.org="">: >>>>> >>>>> Dear Maintainer, >>>>> >>>>> I downloaded available NimbleGen 'single channel' 532.PAIR files for a >>>>> custom built expression microarray from NCBI/GEO (GPL11164). However, I get >>>>> an error message when I try to make the annotation for this platform using >>>>> pdInfoBuild. >>>>> >>>>> In pdInfoBuilder Reference Manual (June 5, 2013), under the >>>>> NgsExpressionPDInfoPkgSeed method, there is a slot for pairFile, although, >>>>> showClasses("Ngs.."), does not show a slot for this, only, XYS. Thus, I >>>>> changed the .pair file extension to .xys. >>>>> >>>>> (ndf<- list.files(getwd(), pattern=".ndf", full.names=TRUE)) # read >>>>> annotation file >>>>> [1] "C:/Users/franklin.johnson.PW99-WEN/Desktop/Test/Yanmin's Microarray >>>>> Paper/Yanmin Microarray RAW/GPL11164.ndf" >>>>> >>>>> (xys <- list.files(getwd(), pattern = ".xys", full.names = TRUE)[1]) >>>>> [1] "C:/Users/franklin.johnson.PW99-WEN/Desktop/Test/Yanmin's Microarray >>>>> Paper/Yanmin Microarray RAW/GSM618107_14418002_532.xys" >>>>> >>>>> But, doing this resulted in an error message: >>>>> seed <- new("NgsExpressionPDInfoPkgSeed", ndfFile = ndf, xysFile = xys, >>>>> author = "FJ", organism = "Apple", species = "Malus x Domestica cv.GD") >>>>> >>>>> makePdInfoPackage(arrays, destDir = getwd()) >>>>> >>>>> ================================================================ ====================================================================== ====== >>>>> Building annotation package for Nimblegen Expression Array >>>>> NDF: GPL11164.ndf >>>>> XYS: GSM618107_14418002_532.xys >>>>> >>>>> ================================================================ ====================================================================== ====== >>>>> Parsing file: GPL11164.ndf... OK >>>>> Parsing file: GSM618107_14418002_532.xys... OK >>>>> Merging NDF and XYS files... OK >>>>> Preparing contents for featureSet table... Error in >>>>> `[.data.frame`(ndfdata, , colsFS) : undefined columns selected >>>>> In addition: Warning message: >>>>> In is.na(ndfdata[["SIGNAL"]]) : >>>>> is.na() applied to non-(list or vector) of type 'NULL' >>>>> >>>>> The only files available from NCBI/GEO are 24 PAIR files and 1 ndf. It >>>>> seems .xys has a different arrangement than .pair, thus .ndf is not >>>>> applicable to annotate the .pair file? Any suggestions? >>>>> Hope to hear from you soon. >>>>> Franklin >>>>> >>>>> -- output of sessionInfo(): >>>>> >>>>>> sessionInfo() >>>>> R version 3.0.1 (2013-05-16) >>>>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>>>> >>>>> locale: >>>>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >>>>> States.1252 LC_MONETARY=English_United States.1252 >>>>> [4] LC_NUMERIC=C LC_TIME=English_United >>>>> States.1252 >>>>> >>>>> attached base packages: >>>>> [1] tcltk grid parallel stats graphics grDevices utils >>>>> datasets methods base >>>>> >>>>> other attached packages: >>>>> [1] pdInfoBuilder_1.24.0 oligo_1.24.0 oligoClasses_1.22.0 >>>>> affxparser_1.32.1 RSQLite_0.11.4 DBI_0.2-7 >>>>> [7] Mfuzz_2.18.0 DynDoc_1.38.0 widgetTools_1.38.0 >>>>> e1071_1.6-1 class_7.3-7 gplots_2.11.0.1 >>>>> [13] KernSmooth_2.23-10 caTools_1.14 gdata_2.12.0.2 >>>>> gtools_2.7.1 timecourse_1.32.0 MASS_7.3-26 >>>>> [19] Biobase_2.20.0 BiocGenerics_0.6.0 limma_3.16.5 >>>>> ggplot2_0.9.3.1 BiocInstaller_1.10.1 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] affyio_1.28.0 Biostrings_2.28.0 bit_1.1-10 >>>>> bitops_1.0-5 codetools_0.2-8 colorspace_1.2-2 >>>>> [7] dichromat_2.0-0 digest_0.6.3 ff_2.2-11 >>>>> foreach_1.4.0 GenomicRanges_1.12.4 gtable_0.1.2 >>>>> [13] IRanges_1.18.1 iterators_1.0.6 labeling_0.1 >>>>> marray_1.38.0 munsell_0.4 plyr_1.8 >>>>> [19] preprocessCore_1.22.0 proto_0.3-10 RColorBrewer_1.0-5 >>>>> reshape2_1.2.2 scales_0.2.3 splines_3.0.1 >>>>> [25] stats4_3.0.1 stringr_0.6.2 tkWidgets_1.38.0 >>>>> tools_3.0.1 zlibbioc_1.6.0 >>>>>> >>>>> >>>>> >>>>> -- >>>>> Sent via the guest posting facility at bioconductor.org. >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>
ADD COMMENTlink written 6.4 years ago by Benilton Carvalho4.3k
Dr. Carvalho, Sorry that was my fault. Yea. I tried that way at first. But got the message below. > rawData=read.xysfiles(filelist, pkgname="pd.pdinfo.gpl11164.ndf.txt") All the XYS files must be of the same type. Error: checkChipTypes(filenames, verbose, "nimblegen") is not TRUE The logical for check.names is giving the error. Perhaps one of my files is incorrect, which I checked and will triple check... I tried check.names=FALSE as the error seemed to be a logical on the platform type: > rawData=read.xysfiles(filelist, pkgname="pd.pdinfo.gpl11164.ndf.txt", check.names=F) Error: These do not exist: FALSE The XYS files did not work either and gave the same result as xys.txt. > xys.files=list.xysfiles(getwd(), full.names=TRUE) > xys.files [1] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/01.xys" [2] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/02.xys" [3] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/03.xys" [4] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/04.xys" [5] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/05.xys" [6] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/06.xys" [7] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/07.xys" [8] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/08.xys" [9] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/09.xys" [10] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/10.xys" [11] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/11.xys" [12] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/12.xys" > basename(xys.files) [1] "01.xys" "02.xys" "03.xys" "04.xys" "05.xys" "06.xys" "07.xys" "08.xys" "09.xys" "10.xys" "11.xys" "12.xys" > ripe=read.xysfiles(xys.files, phenoData=pd) All the XYS files must be of the same type. Error: checkChipTypes(filenames, verbose, "nimblegen") is not TRUE All XYS files are approximately the same size. So, I see no error with making the XYS files. Given the error, again, it seems like a logical argument on the check.names for the platform type. What do you think? Regards, Franklin ________________________________________ From: Benilton Carvalho [beniltoncarvalho@gmail.com] Sent: Wednesday, June 19, 2013 8:53 PM To: Johnson, Franklin Theodore Cc: bioconductor at r-project.org Subject: Re: FeatureExpressionSet using list.files() in place of read.xysfiles() Dear Franklin, I'm not sure I follow your message... my most sincere apologies... Now that you have your XYS files, I was expecting you to simply use: library(oligo) rawData = read.xysfiles(filelist, pkgname='pd.pdinfo.gpl11164.ndf.txt') doesn't this work for you? (the 'filelist' variable above contains the names of your converted XYS files) Let me know what are your findings... b 2013/6/19 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: > Dear Dr. Carvalho, > > Thanks for the reply. > I saw the thread of FAQs how to read in the annotation package made using pdInfoBuilder. > For anyone having issues, it seems as straight forward as: > #install pdinfo.gpl11164.ndf.txt > install.packages("pd.pdinfo.gpl11164.ndf.txt", type="source", repos=NULL) > Installing package into ?C:/Users/ZHUGRP/Documents/R/win- library/3.0? > (as ?lib? is unspecified) > * installing *source* package 'pd.pdinfo.gpl11164.ndf.txt' ... > ** R > ** data > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices > ** testing if installed package can be loaded > *** arch - i386 > *** arch - x64 > * DONE (pd.pdinfo.gpl11164.ndf.txt) > #################################################################### ######################################## > I am currently trying to make the FeatureExpressionSet with my converted PAIR -> XYS.txt files unfortunately obtaining X/Y/S only. > NimbleScan expected .tiff files to read into the software. These files were not available from NCBI/GEO. NimbleGen also did not respond to my inquiry regarding this matter to be able to obtain XYS files from available PAIR files. Using R, I'm testing 12 of 24 tab-delimited XYS files, to also test the annotation package made using pdInfoBuilder. > #read in files from wd() > filelist=list.files(pattern=".*.txt") >> filelist > [1] "GSM01.txt" "GSM02.txt" "GSM03.txt" "GSM04.txt" "GSM05.txt" "GSM06.txt" "GSM07.txt" "GSM08.txt" "GSM09.txt" "GSM10.txt" "GSM11.txt" "GSM12.txt" > #read in each data file in filelist as a matrix to make EFS object >> datalist=lapply(filelist, function(x)as.matrix(read.table(x, header=T, sep="\t", as.is=T))) > #construct phenoData frame >> theData=data.frame(Key=rep(c("Week0","Week-2","Week-4"), each=4)) >> rownames(theData)=basename(filelist) >> pd=new("AnnotatedDataFrame", data=theData) > .... > However, I fail the EFS construction: > hardline=new("ExpressionFeatureSet", datalist, phenoData=pd, annotation=library(pd.pdinfo.gpl11164.ndf.txt)) > Error in .names_found_unique(names(value), names(object)) : > 'sampleNames' replacement list must have unique named elements corresponding to assayData element names > To confirm, >> sampleNames(datalist) > [1] "X" "Y" "PM" > So, it seems EFS is expecting unique sampleNames for each file in filelist? > How to read in multiple files into an efs object, as is done with read.xysfiles? Is this doable? > > Is it necessary to execute datalist=lapply(filelist, function(x)as.matrix(read.table(x, header=T, sep="\t", as.is=T))) surrounded with Booleans to make the object TRUE, per se? > i.e. (datalist=lapply(filelist, function(x)as.matrix(read.table(x, header=T, sep="\t", as.is=T))) ) > Best Regards, > Franklin > > Great minds discuss ideas. Average minds discuss events. Small minds discuss people. -Eleanor Roosevelt > > > > > ________________________________________ > From: Benilton Carvalho [beniltoncarvalho at gmail.com] > Sent: Thursday, June 13, 2013 4:43 PM > To: Johnson, Franklin Theodore > Cc: bioconductor at r-project.org > Subject: Re: [BioC] PAIR files -- feature set table > > dont worry about that particular warning.... just install the package > and try to read your XYS files. > > 2013/6/13 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: >> Dr. Carvalho, >> >> Yes. I see what you mean. >> Switching the columns helped in the FeatureSet table loading inserted more >> that 2 rows: >> >> Inserting 198661 rows into table featureSet... OK >> However, the warning message did print again. >> >> >> Warning message: >> In is.na(ndfdata[["SIGNAL"]]) : >> is.na() applied to non-(list or vector) of type 'NULL' >> >> Below is the output + sessionInfo(), as I upgraded to R 3.0.1. >> >> #Begin R command line code: >> >>> makePdInfoPackage(arrays, destDir = getwd(), unlink=TRUE) >> =================================================================== ====================================================================== ===================== >> >> >> Building annotation package for Nimblegen Expression Array >> NDF: pdinfo_GPL11164.ndf.txt <-new .ndf file with PROBE_ID<->SEQ_ID >> XYS: XYS.txt >> =================================================================== ====================================================================== ===================== >> Parsing file: pdinfo_GPL11164.ndf.txt... OK >> >> Parsing file: XYS.txt... OK >> Merging NDF and XYS files... OK >> Preparing contents for featureSet table... OK >> Preparing contents for bgfeature table... OK >> Preparing contents for pmfeature table... OK >> Creating package in E:/RANDOM/Test/Yanmin's Microarray Paper/Yanmin >> Microarray RAW/pd.pdinfo.gpl11164.ndf.txt >> Inserting 198661 rows into table featureSet... OK >> Inserting 770599 rows into table pmfeature... OK >> >> Counting rows in featureSet >> Counting rows in pmfeature >> Creating index idx_pmfsetid on pmfeature... OK >> Creating index idx_pmfid on pmfeature... OK >> Creating index idx_fsfsetid on featureSet... OK >> Saving DataFrame object for PM. >> Done. >> Warning message: >> In is.na(ndfdata[["SIGNAL"]]) : >> is.na() applied to non-(list or vector) of type 'NULL' >> >> >>> sessionInfo() >> R version 3.0.1 (2013-05-16) >> Platform: i386-w64-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> States.1252 LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C LC_TIME=English_United >> States.1252 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] pdInfoBuilder_1.24.0 oligo_1.24.0 oligoClasses_1.22.0 >> affxparser_1.32.1 RSQLite_0.11.4 DBI_0.2-7 >> Biobase_2.20.0 >> [8] BiocGenerics_0.6.0 BiocInstaller_1.10.2 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.28.0 Biostrings_2.28.0 bit_1.1-10 >> codetools_0.2-8 ff_2.2-11 foreach_1.4.1 >> GenomicRanges_1.12.4 >> [8] IRanges_1.18.1 iterators_1.0.6 preprocessCore_1.22.0 >> splines_3.0.1 stats4_3.0.1 tools_3.0.1 >> zlibbioc_1.6.0 >> >> >> >>>q() >> >> >> >> The built pdInfopackage loaded in Destdir is identical to previous message. >> >> However the featureSet table now has more than 2 rows... >> >> Lastly, I did multiple combos, as my merged file has (X.x, Y.x)<-seems to be >> identifiers for the 'probe IDs' on the array as well as (X.y, Y.y) <- seems >> to be the sequence identifiers for the "SEQ_ID". I used X.x, Y.x and PM >> which gave the result I pasted above. All others had errors. I'm close, but >> that Warning Message is annoying... >> >> >> >> Regards, >> >> Franklin >> >> >> Great minds discuss ideas. Average minds discuss events. Small minds discuss >> people. -Eleanor Roosevelt >> >> >> >> >> ________________________________________ >> From: Benilton Carvalho [beniltoncarvalho at gmail.com] >> Sent: Wednesday, June 12, 2013 8:25 PM >> >> To: Johnson, Franklin Theodore >> Cc: bioconductor at r-project.org >> Subject: Re: [BioC] PAIR files -- feature set table >> >> That does not look ok. >> >> The problem is the count for the featureSet table... This table stores >> the information for "genes" (or whatever the target for this >> particular array is)... so, it is unlikely that you have a microarray >> with only 2 "target units"... I'd expect something around the >> thousands... >> >> pdInfoBuilder uses the information in SEQ_ID (in the NDF) to get the >> target information (i.e., the contents for featureSet). >> >> Given that this is a custom array, I believe that the best idea is to >> contact the person who designed it and ask more details about the >> design (in particular, how many probesets and average number of probes >> per probeset)... >> >> I've seen some designs in which the information that was expected to >> be in SEQ_ID was actually stored in PROBE_ID (in such cases, the user >> needs to create a backup copy of the NDF, and then move the contents >> of PROBE_ID to SEQ_ID - and vice-versa). >> >> b >> >> 2013/6/12 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: >>> Dear Dr. Carvalho, >>> >>> Recently, we had cooresponence regaring makePDInfoPackage for an NimbleGen >>> apple microarray. >>> I was able to merge the ndf design and XYS files using PROBE_ID. >>> As a reminder this is a custom array, and there are no SIGNAL==NAs for >>> control probes. >>> It seemed to work: >>>> makePdInfoPackage(seed, destDir("")) >>> >>> ================================================================== ====================================================================== ==================== >>> Building annotation package for Nimblegen Expression Array >>> NDF: GPL11164.ndf >>> XYS: XYS.txt >>> >>> ================================================================== ====================================================================== ==================== >>> Parsing file: GPL11164.ndf... OK >>> Parsing file: XYS.txt... OK >>> Merging NDF and XYS files... OK >>> Preparing contents for featureSet table... OK >>> Preparing contents for bgfeature table... OK >>> Preparing contents for pmfeature table... OK >>> Creating package in >>> C:/Users/franklin.johnson.PW50-WEN/Desktop/Test/Yanmin's Microarray >>> Paper/Yanmin Microarray RAW/pd.gpl11164 >>> Inserting 2 rows into table featureSet... OK >>> Inserting 765524 rows into table pmfeature... OK >>> Inserting 5075 rows into table bgfeature... OK >>> Counting rows in bgfeature >>> Counting rows in featureSet >>> Counting rows in pmfeature >>> Creating index idx_bgfsetid on bgfeature... OK >>> Creating index idx_bgfid on bgfeature... OK >>> Creating index idx_pmfsetid on pmfeature... OK >>> Creating index idx_pmfid on pmfeature... OK >>> Creating index idx_fsfsetid on featureSet... OK >>> Saving DataFrame object for PM. >>> Saving DataFrame object for BG. >>> Done. >>> Warning message: >>> In is.na(ndfdata[["SIGNAL"]]) : >>> is.na() applied to non-(list or vector) of type 'NULL' >>>> >>> >>> In contrast to this warning message, I see a pdinfopackage directory with >>> 4 subdirectories: c=("data", "inst", "man", R"), as well as >>> subsubdirectories in "inst"=c("extdata", and "Unit Tests"), in addition to >>> two text files in the main directory: c=("DESCRIPTION", "NAMESPACE") were >>> created in my destination folder. >>> Before using "oligo", if possible, I wanted to confirm with you that this >>> package is viable to use with "oligo" although a warning message that may >>> not pertain to my custom designed microarray was printed. >>> >>> Regards, >>> Franklin >>> >>> Great minds discuss ideas. Average minds discuss events. Small minds >>> discuss people. -Eleanor Roosevelt >>> >>> >>> >>> >>> ________________________________________ >>> From: Johnson, Franklin Theodore >>> Sent: Friday, June 07, 2013 10:39 AM >>> To: Benilton Carvalho >>> Cc: bioconductor at r-project.org >>> Subject: RE: [BioC] PAIR files -- feature set table >>> >>> Resending to bioconductor message thread: >>> >>> Dear Dr. Carvalho, >>> Thanks for the response. >>> As you suggested, I will look into the merge function using "Probe_ID". >>> After reading in the data, I will start here: merge.datasets(dataset1, >>> dataset2, by="key"). >>> Best Regards, >>> Franklin >>> >>> Great minds discuss ideas. Average minds discuss events. Small minds >>> discuss people. -Eleanor Roosevelt >>> >>> ________________________________________ >>> From: Benilton Carvalho [beniltoncarvalho at gmail.com] >>> Sent: Thursday, June 06, 2013 8:11 PM >>> To: Johnson, Franklin Theodore >>> Cc: bioconductor at r-project.org; franklin.johnson at wsu.edu >>> Subject: Re: [BioC] PAIR files -- feature set table >>> >>> You will need to merge the PAIR and the NDF using the PROBE_ID column >>> as key. This will allow you to get the X/Y coordinates needed to >>> create the XYS as described on the other messages. >>> >>> Regarding annotation, you may need to contact NimbleGen to request >>> this information directly from them... >>> >>> benilton >>> >>> 2013/6/6 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: >>>> Dear Dr. Carvalho, >>>> >>>> Muchos grasias for the reply. >>>> >>>> Actually, this is what my .ndf file looks like: >>>>> head(ndf) >>>> PROBE_DESIGN_ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA SEQ_ID >>>> 1 7552_0343_0009 Duplicate_1 >>>> 2 7552_0345_0009 Duplicate_2 >>>> 3 7552_0347_0009 Duplicate_1 >>>> 4 7552_0349_0009 Duplicate_2 >>>> 5 7552_0351_0009 Duplicate_2 >>>> 6 7552_0353_0009 Duplicate_1 >>>> PROBE_SEQUENCE MISMATCH >>>> MATCH_INDEX FEATURE_ID ROW_NUM COL_NUM PROBE_CLASS >>>> 1 cttgactcttctaagttcaaaggtaactcaagtgaagctgtcagatatgatccttcca 0 >>>> 64535488 64535488 9 343 >>>> 2 cccaagcattaaaccttactcatatacttataatgcagccatcaagagtttgtgcaagg 0 >>>> 64799310 64799310 9 345 >>>> 3 agggaggctgaaagagagagtgaatggtccagctgggcataattgctgca 0 >>>> 64476989 64476989 9 347 >>>> 4 ttgttggtgggggtgttgcccttagtaccccagaccttgaagcagttaaa 0 >>>> 64862794 64862794 9 349 >>>> 5 gtgtggggccccctttctttaactggaacctttctttgaagcaatttggg 0 >>>> 64832726 64832726 9 351 >>>> 6 ttgtccaattccaacatgccgagacggcagggattgtgatcgtgttgttc 0 >>>> 64435686 64435686 9 353 >>>> PROBE_ID POSITION DESIGN_ID X Y >>>> 1 Contig19819_1_f_28_10_535 0 7552 343 9 >>>> 2 Malus_CN899188_2_f_147_1_755 0 7552 345 9 >>>> 3 Contig20738_8_r_1179_2_1432 0 7552 347 9 >>>> 4 Malus_CN880097_2_r_336_2_536 0 7552 349 9 >>>> 5 Malus_CN918117_2_f_632_1_781 0 7552 351 9 >>>> 6 Contig1991_1_f_71_2_1239 0 7552 353 9 >>>> >>>> The pair files, .532 pair files only (one-color arrays), only obtain the >>>> probe ID and signal; after some text at the top describing the experiment. >>>> My real issue is that I can further normalize and analyze the RMA files with >>>> sva and limma, etc. However, I cannot annotate the probes without the array >>>> annotation, as there are duplicates in the ndf file which are removed in the >>>> RMA.pair files available on NCBI/GEO. So they will not match in any >>>> annotation package I've failed at trying. >>>> So, I' tried to go back and start from the raw pair files...this custom >>>> array is really a "custom" array without >>>> NimbleScan. >>>> >>>> Salud, >>>> Franklin >>>> >>>> >>>> >>>> >>>> >>>> >>>> Great minds discuss ideas. Average minds discuss events. Small minds >>>> discuss people. -Eleanor Roosevelt >>>> >>>> >>>> >>>> >>>> ________________________________________ >>>> From: Benilton Carvalho [beniltoncarvalho at gmail.com] >>>> Sent: Wednesday, June 05, 2013 6:42 PM >>>> To: FRANKLIN JOHNSON [guest] >>>> Cc: bioconductor at r-project.org; franklin.johnson at wsu.edu; pdInfoBuilder >>>> Maintainer >>>> Subject: Re: [BioC] PAIR files -- feature set table >>>> >>>> It's an unfortunate mistake to have the pairFile *argument* in the >>>> call (not in the slots session, but I see your point). :-( I'll make >>>> sure that this is fixed. >>>> >>>> You need to convert the PAIR files to XYS... >>>> >>>> Some refs that should help you in the process: >>>> >>>> https://stat.ethz.ch/pipermail/bioconductor/2012-January/043186.html >>>> >>>> http://comments.gmane.org/gmane.science.biology.informatics.condu ctor/27547 >>>> >>>> b >>>> >>>> 2013/6/5 FRANKLIN JOHNSON [guest] <guest at="" bioconductor.org="">: >>>>> >>>>> Dear Maintainer, >>>>> >>>>> I downloaded available NimbleGen 'single channel' 532.PAIR files for a >>>>> custom built expression microarray from NCBI/GEO (GPL11164). However, I get >>>>> an error message when I try to make the annotation for this platform using >>>>> pdInfoBuild. >>>>> >>>>> In pdInfoBuilder Reference Manual (June 5, 2013), under the >>>>> NgsExpressionPDInfoPkgSeed method, there is a slot for pairFile, although, >>>>> showClasses("Ngs.."), does not show a slot for this, only, XYS. Thus, I >>>>> changed the .pair file extension to .xys. >>>>> >>>>> (ndf<- list.files(getwd(), pattern=".ndf", full.names=TRUE)) # read >>>>> annotation file >>>>> [1] "C:/Users/franklin.johnson.PW99-WEN/Desktop/Test/Yanmin's Microarray >>>>> Paper/Yanmin Microarray RAW/GPL11164.ndf" >>>>> >>>>> (xys <- list.files(getwd(), pattern = ".xys", full.names = TRUE)[1]) >>>>> [1] "C:/Users/franklin.johnson.PW99-WEN/Desktop/Test/Yanmin's Microarray >>>>> Paper/Yanmin Microarray RAW/GSM618107_14418002_532.xys" >>>>> >>>>> But, doing this resulted in an error message: >>>>> seed <- new("NgsExpressionPDInfoPkgSeed", ndfFile = ndf, xysFile = xys, >>>>> author = "FJ", organism = "Apple", species = "Malus x Domestica cv.GD") >>>>> >>>>> makePdInfoPackage(arrays, destDir = getwd()) >>>>> >>>>> ================================================================ ====================================================================== ====== >>>>> Building annotation package for Nimblegen Expression Array >>>>> NDF: GPL11164.ndf >>>>> XYS: GSM618107_14418002_532.xys >>>>> >>>>> ================================================================ ====================================================================== ====== >>>>> Parsing file: GPL11164.ndf... OK >>>>> Parsing file: GSM618107_14418002_532.xys... OK >>>>> Merging NDF and XYS files... OK >>>>> Preparing contents for featureSet table... Error in >>>>> `[.data.frame`(ndfdata, , colsFS) : undefined columns selected >>>>> In addition: Warning message: >>>>> In is.na(ndfdata[["SIGNAL"]]) : >>>>> is.na() applied to non-(list or vector) of type 'NULL' >>>>> >>>>> The only files available from NCBI/GEO are 24 PAIR files and 1 ndf. It >>>>> seems .xys has a different arrangement than .pair, thus .ndf is not >>>>> applicable to annotate the .pair file? Any suggestions? >>>>> Hope to hear from you soon. >>>>> Franklin >>>>> >>>>> -- output of sessionInfo(): >>>>> >>>>>> sessionInfo() >>>>> R version 3.0.1 (2013-05-16) >>>>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>>>> >>>>> locale: >>>>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >>>>> States.1252 LC_MONETARY=English_United States.1252 >>>>> [4] LC_NUMERIC=C LC_TIME=English_United >>>>> States.1252 >>>>> >>>>> attached base packages: >>>>> [1] tcltk grid parallel stats graphics grDevices utils >>>>> datasets methods base >>>>> >>>>> other attached packages: >>>>> [1] pdInfoBuilder_1.24.0 oligo_1.24.0 oligoClasses_1.22.0 >>>>> affxparser_1.32.1 RSQLite_0.11.4 DBI_0.2-7 >>>>> [7] Mfuzz_2.18.0 DynDoc_1.38.0 widgetTools_1.38.0 >>>>> e1071_1.6-1 class_7.3-7 gplots_2.11.0.1 >>>>> [13] KernSmooth_2.23-10 caTools_1.14 gdata_2.12.0.2 >>>>> gtools_2.7.1 timecourse_1.32.0 MASS_7.3-26 >>>>> [19] Biobase_2.20.0 BiocGenerics_0.6.0 limma_3.16.5 >>>>> ggplot2_0.9.3.1 BiocInstaller_1.10.1 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] affyio_1.28.0 Biostrings_2.28.0 bit_1.1-10 >>>>> bitops_1.0-5 codetools_0.2-8 colorspace_1.2-2 >>>>> [7] dichromat_2.0-0 digest_0.6.3 ff_2.2-11 >>>>> foreach_1.4.0 GenomicRanges_1.12.4 gtable_0.1.2 >>>>> [13] IRanges_1.18.1 iterators_1.0.6 labeling_0.1 >>>>> marray_1.38.0 munsell_0.4 plyr_1.8 >>>>> [19] preprocessCore_1.22.0 proto_0.3-10 RColorBrewer_1.0-5 >>>>> reshape2_1.2.2 scales_0.2.3 splines_3.0.1 >>>>> [25] stats4_3.0.1 stringr_0.6.2 tkWidgets_1.38.0 >>>>> tools_3.0.1 zlibbioc_1.6.0 >>>>>> >>>>> >>>>> >>>>> -- >>>>> Sent via the guest posting facility at bioconductor.org. >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>
ADD REPLYlink written 6.4 years ago by Johnson, Franklin Theodore140
Dr. Carvalho, Sorry to get back to you first. According to previous posts, http://comments.gmane.org/gmane.science.b iology.informatics.conductor/35367 I think it the XYS file error above may be related to the pdInfoBuilder annotation package, pd.pdinfo.gpl11164.ndf.txt. I went back to make the build the package again using the XYS file. I get the [[SIGNAL]] error although PROBE_ID <-> SEQ_ID in the NDF file as per previous email in this thread. Perhaps this is because XYS is sorted 1,1; 1,2; 2,1; 2,2; 3,1; 3,2....but the NDF is not? ====================================================================== ================================================ Building annotation package for Nimblegen Expression Array NDF: GPL11164.ndf XYS: 01.xys ====================================================================== ================================================ Parsing file: GPL11164.ndf... OK Parsing file: 01.xys... OK Merging NDF and XYS files... OK Preparing contents for featureSet table... OK Preparing contents for bgfeature table... OK Preparing contents for pmfeature table... OK Error in parseNgsPair(object at ndfFile, object at xysFile, verbose = !quiet) : Control probe possibly identified as Experimental In addition: Warning message: In is.na(ndfdata[["SIGNAL"]]) : is.na() applied to non-(list or vector) of type 'NULL' As I take a closer look at the ndf file, I do see control probes in the ndf file that are not present in the merged PAIR-XYS files. These are held in CONTAINER= 'NGS_CONTROLS' with PROBE_ID = XENOSYNTH0040, MISMATCH=10007. However, !is.na()=TRUE throughout the NDF file. Here is another line representing the CONTROLS: PROBE_DESIGN_ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA SEQ_ID PROBE_SEQUENCE MISMATCH MATCH_INDEX FEATURE_ID ROW_NUM COL_NUM PROBE_CLASS PROBE_ID POSITION DESIGN_ID X Y 7552_0712_1000 NGS_CONTROLS EMPTY dark EMPTY N 0 62990761 62990761 1000 712 control EMPTY 0 7552 712 1000 I will look at previous threads that may have mentioned just removing these CONTROLS from the NDF file. In addition to CONTROLS, there are BLOCK1 and RANDOM types as well. These additional two types can be found in the PAIR file. Hope to hear from you soon. Bittersweet! Franklin Great minds discuss ideas. Average minds discuss events. Small minds discuss people. -Eleanor Roosevelt ________________________________________ From: Johnson, Franklin Theodore Sent: Wednesday, June 19, 2013 11:25 PM To: Benilton Carvalho Cc: bioconductor at r-project.org Subject: RE: FeatureExpressionSet using list.files() in place of read.xysfiles() Dr. Carvalho, Sorry that was my fault. Yea. I tried that way at first. But got the message below. > rawData=read.xysfiles(filelist, pkgname="pd.pdinfo.gpl11164.ndf.txt") All the XYS files must be of the same type. Error: checkChipTypes(filenames, verbose, "nimblegen") is not TRUE The logical for check.names is giving the error. Perhaps one of my files is incorrect, which I checked and will triple check... I tried check.names=FALSE as the error seemed to be a logical on the platform type: > rawData=read.xysfiles(filelist, pkgname="pd.pdinfo.gpl11164.ndf.txt", check.names=F) Error: These do not exist: FALSE The XYS files did not work either and gave the same result as xys.txt. > xys.files=list.xysfiles(getwd(), full.names=TRUE) > xys.files [1] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/01.xys" [2] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/02.xys" [3] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/03.xys" [4] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/04.xys" [5] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/05.xys" [6] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/06.xys" [7] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/07.xys" [8] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/08.xys" [9] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/09.xys" [10] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/10.xys" [11] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/11.xys" [12] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/12.xys" > basename(xys.files) [1] "01.xys" "02.xys" "03.xys" "04.xys" "05.xys" "06.xys" "07.xys" "08.xys" "09.xys" "10.xys" "11.xys" "12.xys" > ripe=read.xysfiles(xys.files, phenoData=pd) All the XYS files must be of the same type. Error: checkChipTypes(filenames, verbose, "nimblegen") is not TRUE All XYS files are approximately the same size. So, I see no error with making the XYS files. Given the error, again, it seems like a logical argument on the check.names for the platform type. What do you think? Regards, Franklin ________________________________________ From: Benilton Carvalho [beniltoncarvalho@gmail.com] Sent: Wednesday, June 19, 2013 8:53 PM To: Johnson, Franklin Theodore Cc: bioconductor at r-project.org Subject: Re: FeatureExpressionSet using list.files() in place of read.xysfiles() Dear Franklin, I'm not sure I follow your message... my most sincere apologies... Now that you have your XYS files, I was expecting you to simply use: library(oligo) rawData = read.xysfiles(filelist, pkgname='pd.pdinfo.gpl11164.ndf.txt') doesn't this work for you? (the 'filelist' variable above contains the names of your converted XYS files) Let me know what are your findings... b 2013/6/19 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: > Dear Dr. Carvalho, > > Thanks for the reply. > I saw the thread of FAQs how to read in the annotation package made using pdInfoBuilder. > For anyone having issues, it seems as straight forward as: > #install pdinfo.gpl11164.ndf.txt > install.packages("pd.pdinfo.gpl11164.ndf.txt", type="source", repos=NULL) > Installing package into ?C:/Users/ZHUGRP/Documents/R/win- library/3.0? > (as ?lib? is unspecified) > * installing *source* package 'pd.pdinfo.gpl11164.ndf.txt' ... > ** R > ** data > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices > ** testing if installed package can be loaded > *** arch - i386 > *** arch - x64 > * DONE (pd.pdinfo.gpl11164.ndf.txt) > #################################################################### ######################################## > I am currently trying to make the FeatureExpressionSet with my converted PAIR -> XYS.txt files unfortunately obtaining X/Y/S only. > NimbleScan expected .tiff files to read into the software. These files were not available from NCBI/GEO. NimbleGen also did not respond to my inquiry regarding this matter to be able to obtain XYS files from available PAIR files. Using R, I'm testing 12 of 24 tab-delimited XYS files, to also test the annotation package made using pdInfoBuilder. > #read in files from wd() > filelist=list.files(pattern=".*.txt") >> filelist > [1] "GSM01.txt" "GSM02.txt" "GSM03.txt" "GSM04.txt" "GSM05.txt" "GSM06.txt" "GSM07.txt" "GSM08.txt" "GSM09.txt" "GSM10.txt" "GSM11.txt" "GSM12.txt" > #read in each data file in filelist as a matrix to make EFS object >> datalist=lapply(filelist, function(x)as.matrix(read.table(x, header=T, sep="\t", as.is=T))) > #construct phenoData frame >> theData=data.frame(Key=rep(c("Week0","Week-2","Week-4"), each=4)) >> rownames(theData)=basename(filelist) >> pd=new("AnnotatedDataFrame", data=theData) > .... > However, I fail the EFS construction: > hardline=new("ExpressionFeatureSet", datalist, phenoData=pd, annotation=library(pd.pdinfo.gpl11164.ndf.txt)) > Error in .names_found_unique(names(value), names(object)) : > 'sampleNames' replacement list must have unique named elements corresponding to assayData element names > To confirm, >> sampleNames(datalist) > [1] "X" "Y" "PM" > So, it seems EFS is expecting unique sampleNames for each file in filelist? > How to read in multiple files into an efs object, as is done with read.xysfiles? Is this doable? > > Is it necessary to execute datalist=lapply(filelist, function(x)as.matrix(read.table(x, header=T, sep="\t", as.is=T))) surrounded with Booleans to make the object TRUE, per se? > i.e. (datalist=lapply(filelist, function(x)as.matrix(read.table(x, header=T, sep="\t", as.is=T))) ) > Best Regards, > Franklin > > Great minds discuss ideas. Average minds discuss events. Small minds discuss people. -Eleanor Roosevelt > > > > > ________________________________________ > From: Benilton Carvalho [beniltoncarvalho at gmail.com] > Sent: Thursday, June 13, 2013 4:43 PM > To: Johnson, Franklin Theodore > Cc: bioconductor at r-project.org > Subject: Re: [BioC] PAIR files -- feature set table > > dont worry about that particular warning.... just install the package > and try to read your XYS files. > > 2013/6/13 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: >> Dr. Carvalho, >> >> Yes. I see what you mean. >> Switching the columns helped in the FeatureSet table loading inserted more >> that 2 rows: >> >> Inserting 198661 rows into table featureSet... OK >> However, the warning message did print again. >> >> >> Warning message: >> In is.na(ndfdata[["SIGNAL"]]) : >> is.na() applied to non-(list or vector) of type 'NULL' >> >> Below is the output + sessionInfo(), as I upgraded to R 3.0.1. >> >> #Begin R command line code: >> >>> makePdInfoPackage(arrays, destDir = getwd(), unlink=TRUE) >> =================================================================== ====================================================================== ===================== >> >> >> Building annotation package for Nimblegen Expression Array >> NDF: pdinfo_GPL11164.ndf.txt <-new .ndf file with PROBE_ID<->SEQ_ID >> XYS: XYS.txt >> =================================================================== ====================================================================== ===================== >> Parsing file: pdinfo_GPL11164.ndf.txt... OK >> >> Parsing file: XYS.txt... OK >> Merging NDF and XYS files... OK >> Preparing contents for featureSet table... OK >> Preparing contents for bgfeature table... OK >> Preparing contents for pmfeature table... OK >> Creating package in E:/RANDOM/Test/Yanmin's Microarray Paper/Yanmin >> Microarray RAW/pd.pdinfo.gpl11164.ndf.txt >> Inserting 198661 rows into table featureSet... OK >> Inserting 770599 rows into table pmfeature... OK >> >> Counting rows in featureSet >> Counting rows in pmfeature >> Creating index idx_pmfsetid on pmfeature... OK >> Creating index idx_pmfid on pmfeature... OK >> Creating index idx_fsfsetid on featureSet... OK >> Saving DataFrame object for PM. >> Done. >> Warning message: >> In is.na(ndfdata[["SIGNAL"]]) : >> is.na() applied to non-(list or vector) of type 'NULL' >> >> >>> sessionInfo() >> R version 3.0.1 (2013-05-16) >> Platform: i386-w64-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> States.1252 LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C LC_TIME=English_United >> States.1252 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] pdInfoBuilder_1.24.0 oligo_1.24.0 oligoClasses_1.22.0 >> affxparser_1.32.1 RSQLite_0.11.4 DBI_0.2-7 >> Biobase_2.20.0 >> [8] BiocGenerics_0.6.0 BiocInstaller_1.10.2 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.28.0 Biostrings_2.28.0 bit_1.1-10 >> codetools_0.2-8 ff_2.2-11 foreach_1.4.1 >> GenomicRanges_1.12.4 >> [8] IRanges_1.18.1 iterators_1.0.6 preprocessCore_1.22.0 >> splines_3.0.1 stats4_3.0.1 tools_3.0.1 >> zlibbioc_1.6.0 >> >> >> >>>q() >> >> >> >> The built pdInfopackage loaded in Destdir is identical to previous message. >> >> However the featureSet table now has more than 2 rows... >> >> Lastly, I did multiple combos, as my merged file has (X.x, Y.x)<-seems to be >> identifiers for the 'probe IDs' on the array as well as (X.y, Y.y) <- seems >> to be the sequence identifiers for the "SEQ_ID". I used X.x, Y.x and PM >> which gave the result I pasted above. All others had errors. I'm close, but >> that Warning Message is annoying... >> >> >> >> Regards, >> >> Franklin >> >> >> Great minds discuss ideas. Average minds discuss events. Small minds discuss >> people. -Eleanor Roosevelt >> >> >> >> >> ________________________________________ >> From: Benilton Carvalho [beniltoncarvalho at gmail.com] >> Sent: Wednesday, June 12, 2013 8:25 PM >> >> To: Johnson, Franklin Theodore >> Cc: bioconductor at r-project.org >> Subject: Re: [BioC] PAIR files -- feature set table >> >> That does not look ok. >> >> The problem is the count for the featureSet table... This table stores >> the information for "genes" (or whatever the target for this >> particular array is)... so, it is unlikely that you have a microarray >> with only 2 "target units"... I'd expect something around the >> thousands... >> >> pdInfoBuilder uses the information in SEQ_ID (in the NDF) to get the >> target information (i.e., the contents for featureSet). >> >> Given that this is a custom array, I believe that the best idea is to >> contact the person who designed it and ask more details about the >> design (in particular, how many probesets and average number of probes >> per probeset)... >> >> I've seen some designs in which the information that was expected to >> be in SEQ_ID was actually stored in PROBE_ID (in such cases, the user >> needs to create a backup copy of the NDF, and then move the contents >> of PROBE_ID to SEQ_ID - and vice-versa). >> >> b >> >> 2013/6/12 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: >>> Dear Dr. Carvalho, >>> >>> Recently, we had cooresponence regaring makePDInfoPackage for an NimbleGen >>> apple microarray. >>> I was able to merge the ndf design and XYS files using PROBE_ID. >>> As a reminder this is a custom array, and there are no SIGNAL==NAs for >>> control probes. >>> It seemed to work: >>>> makePdInfoPackage(seed, destDir("")) >>> >>> ================================================================== ====================================================================== ==================== >>> Building annotation package for Nimblegen Expression Array >>> NDF: GPL11164.ndf >>> XYS: XYS.txt >>> >>> ================================================================== ====================================================================== ==================== >>> Parsing file: GPL11164.ndf... OK >>> Parsing file: XYS.txt... OK >>> Merging NDF and XYS files... OK >>> Preparing contents for featureSet table... OK >>> Preparing contents for bgfeature table... OK >>> Preparing contents for pmfeature table... OK >>> Creating package in >>> C:/Users/franklin.johnson.PW50-WEN/Desktop/Test/Yanmin's Microarray >>> Paper/Yanmin Microarray RAW/pd.gpl11164 >>> Inserting 2 rows into table featureSet... OK >>> Inserting 765524 rows into table pmfeature... OK >>> Inserting 5075 rows into table bgfeature... OK >>> Counting rows in bgfeature >>> Counting rows in featureSet >>> Counting rows in pmfeature >>> Creating index idx_bgfsetid on bgfeature... OK >>> Creating index idx_bgfid on bgfeature... OK >>> Creating index idx_pmfsetid on pmfeature... OK >>> Creating index idx_pmfid on pmfeature... OK >>> Creating index idx_fsfsetid on featureSet... OK >>> Saving DataFrame object for PM. >>> Saving DataFrame object for BG. >>> Done. >>> Warning message: >>> In is.na(ndfdata[["SIGNAL"]]) : >>> is.na() applied to non-(list or vector) of type 'NULL' >>>> >>> >>> In contrast to this warning message, I see a pdinfopackage directory with >>> 4 subdirectories: c=("data", "inst", "man", R"), as well as >>> subsubdirectories in "inst"=c("extdata", and "Unit Tests"), in addition to >>> two text files in the main directory: c=("DESCRIPTION", "NAMESPACE") were >>> created in my destination folder. >>> Before using "oligo", if possible, I wanted to confirm with you that this >>> package is viable to use with "oligo" although a warning message that may >>> not pertain to my custom designed microarray was printed. >>> >>> Regards, >>> Franklin >>> >>> Great minds discuss ideas. Average minds discuss events. Small minds >>> discuss people. -Eleanor Roosevelt >>> >>> >>> >>> >>> ________________________________________ >>> From: Johnson, Franklin Theodore >>> Sent: Friday, June 07, 2013 10:39 AM >>> To: Benilton Carvalho >>> Cc: bioconductor at r-project.org >>> Subject: RE: [BioC] PAIR files -- feature set table >>> >>> Resending to bioconductor message thread: >>> >>> Dear Dr. Carvalho, >>> Thanks for the response. >>> As you suggested, I will look into the merge function using "Probe_ID". >>> After reading in the data, I will start here: merge.datasets(dataset1, >>> dataset2, by="key"). >>> Best Regards, >>> Franklin >>> >>> Great minds discuss ideas. Average minds discuss events. Small minds >>> discuss people. -Eleanor Roosevelt >>> >>> ________________________________________ >>> From: Benilton Carvalho [beniltoncarvalho at gmail.com] >>> Sent: Thursday, June 06, 2013 8:11 PM >>> To: Johnson, Franklin Theodore >>> Cc: bioconductor at r-project.org; franklin.johnson at wsu.edu >>> Subject: Re: [BioC] PAIR files -- feature set table >>> >>> You will need to merge the PAIR and the NDF using the PROBE_ID column >>> as key. This will allow you to get the X/Y coordinates needed to >>> create the XYS as described on the other messages. >>> >>> Regarding annotation, you may need to contact NimbleGen to request >>> this information directly from them... >>> >>> benilton >>> >>> 2013/6/6 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: >>>> Dear Dr. Carvalho, >>>> >>>> Muchos grasias for the reply. >>>> >>>> Actually, this is what my .ndf file looks like: >>>>> head(ndf) >>>> PROBE_DESIGN_ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA SEQ_ID >>>> 1 7552_0343_0009 Duplicate_1 >>>> 2 7552_0345_0009 Duplicate_2 >>>> 3 7552_0347_0009 Duplicate_1 >>>> 4 7552_0349_0009 Duplicate_2 >>>> 5 7552_0351_0009 Duplicate_2 >>>> 6 7552_0353_0009 Duplicate_1 >>>> PROBE_SEQUENCE MISMATCH >>>> MATCH_INDEX FEATURE_ID ROW_NUM COL_NUM PROBE_CLASS >>>> 1 cttgactcttctaagttcaaaggtaactcaagtgaagctgtcagatatgatccttcca 0 >>>> 64535488 64535488 9 343 >>>> 2 cccaagcattaaaccttactcatatacttataatgcagccatcaagagtttgtgcaagg 0 >>>> 64799310 64799310 9 345 >>>> 3 agggaggctgaaagagagagtgaatggtccagctgggcataattgctgca 0 >>>> 64476989 64476989 9 347 >>>> 4 ttgttggtgggggtgttgcccttagtaccccagaccttgaagcagttaaa 0 >>>> 64862794 64862794 9 349 >>>> 5 gtgtggggccccctttctttaactggaacctttctttgaagcaatttggg 0 >>>> 64832726 64832726 9 351 >>>> 6 ttgtccaattccaacatgccgagacggcagggattgtgatcgtgttgttc 0 >>>> 64435686 64435686 9 353 >>>> PROBE_ID POSITION DESIGN_ID X Y >>>> 1 Contig19819_1_f_28_10_535 0 7552 343 9 >>>> 2 Malus_CN899188_2_f_147_1_755 0 7552 345 9 >>>> 3 Contig20738_8_r_1179_2_1432 0 7552 347 9 >>>> 4 Malus_CN880097_2_r_336_2_536 0 7552 349 9 >>>> 5 Malus_CN918117_2_f_632_1_781 0 7552 351 9 >>>> 6 Contig1991_1_f_71_2_1239 0 7552 353 9 >>>> >>>> The pair files, .532 pair files only (one-color arrays), only obtain the >>>> probe ID and signal; after some text at the top describing the experiment. >>>> My real issue is that I can further normalize and analyze the RMA files with >>>> sva and limma, etc. However, I cannot annotate the probes without the array >>>> annotation, as there are duplicates in the ndf file which are removed in the >>>> RMA.pair files available on NCBI/GEO. So they will not match in any >>>> annotation package I've failed at trying. >>>> So, I' tried to go back and start from the raw pair files...this custom >>>> array is really a "custom" array without >>>> NimbleScan. >>>> >>>> Salud, >>>> Franklin >>>> >>>> >>>> >>>> >>>> >>>> >>>> Great minds discuss ideas. Average minds discuss events. Small minds >>>> discuss people. -Eleanor Roosevelt >>>> >>>> >>>> >>>> >>>> ________________________________________ >>>> From: Benilton Carvalho [beniltoncarvalho at gmail.com] >>>> Sent: Wednesday, June 05, 2013 6:42 PM >>>> To: FRANKLIN JOHNSON [guest] >>>> Cc: bioconductor at r-project.org; franklin.johnson at wsu.edu; pdInfoBuilder >>>> Maintainer >>>> Subject: Re: [BioC] PAIR files -- feature set table >>>> >>>> It's an unfortunate mistake to have the pairFile *argument* in the >>>> call (not in the slots session, but I see your point). :-( I'll make >>>> sure that this is fixed. >>>> >>>> You need to convert the PAIR files to XYS... >>>> >>>> Some refs that should help you in the process: >>>> >>>> https://stat.ethz.ch/pipermail/bioconductor/2012-January/043186.html >>>> >>>> http://comments.gmane.org/gmane.science.biology.informatics.condu ctor/27547 >>>> >>>> b >>>> >>>> 2013/6/5 FRANKLIN JOHNSON [guest] <guest at="" bioconductor.org="">: >>>>> >>>>> Dear Maintainer, >>>>> >>>>> I downloaded available NimbleGen 'single channel' 532.PAIR files for a >>>>> custom built expression microarray from NCBI/GEO (GPL11164). However, I get >>>>> an error message when I try to make the annotation for this platform using >>>>> pdInfoBuild. >>>>> >>>>> In pdInfoBuilder Reference Manual (June 5, 2013), under the >>>>> NgsExpressionPDInfoPkgSeed method, there is a slot for pairFile, although, >>>>> showClasses("Ngs.."), does not show a slot for this, only, XYS. Thus, I >>>>> changed the .pair file extension to .xys. >>>>> >>>>> (ndf<- list.files(getwd(), pattern=".ndf", full.names=TRUE)) # read >>>>> annotation file >>>>> [1] "C:/Users/franklin.johnson.PW99-WEN/Desktop/Test/Yanmin's Microarray >>>>> Paper/Yanmin Microarray RAW/GPL11164.ndf" >>>>> >>>>> (xys <- list.files(getwd(), pattern = ".xys", full.names = TRUE)[1]) >>>>> [1] "C:/Users/franklin.johnson.PW99-WEN/Desktop/Test/Yanmin's Microarray >>>>> Paper/Yanmin Microarray RAW/GSM618107_14418002_532.xys" >>>>> >>>>> But, doing this resulted in an error message: >>>>> seed <- new("NgsExpressionPDInfoPkgSeed", ndfFile = ndf, xysFile = xys, >>>>> author = "FJ", organism = "Apple", species = "Malus x Domestica cv.GD") >>>>> >>>>> makePdInfoPackage(arrays, destDir = getwd()) >>>>> >>>>> ================================================================ ====================================================================== ====== >>>>> Building annotation package for Nimblegen Expression Array >>>>> NDF: GPL11164.ndf >>>>> XYS: GSM618107_14418002_532.xys >>>>> >>>>> ================================================================ ====================================================================== ====== >>>>> Parsing file: GPL11164.ndf... OK >>>>> Parsing file: GSM618107_14418002_532.xys... OK >>>>> Merging NDF and XYS files... OK >>>>> Preparing contents for featureSet table... Error in >>>>> `[.data.frame`(ndfdata, , colsFS) : undefined columns selected >>>>> In addition: Warning message: >>>>> In is.na(ndfdata[["SIGNAL"]]) : >>>>> is.na() applied to non-(list or vector) of type 'NULL' >>>>> >>>>> The only files available from NCBI/GEO are 24 PAIR files and 1 ndf. It >>>>> seems .xys has a different arrangement than .pair, thus .ndf is not >>>>> applicable to annotate the .pair file? Any suggestions? >>>>> Hope to hear from you soon. >>>>> Franklin >>>>> >>>>> -- output of sessionInfo(): >>>>> >>>>>> sessionInfo() >>>>> R version 3.0.1 (2013-05-16) >>>>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>>>> >>>>> locale: >>>>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >>>>> States.1252 LC_MONETARY=English_United States.1252 >>>>> [4] LC_NUMERIC=C LC_TIME=English_United >>>>> States.1252 >>>>> >>>>> attached base packages: >>>>> [1] tcltk grid parallel stats graphics grDevices utils >>>>> datasets methods base >>>>> >>>>> other attached packages: >>>>> [1] pdInfoBuilder_1.24.0 oligo_1.24.0 oligoClasses_1.22.0 >>>>> affxparser_1.32.1 RSQLite_0.11.4 DBI_0.2-7 >>>>> [7] Mfuzz_2.18.0 DynDoc_1.38.0 widgetTools_1.38.0 >>>>> e1071_1.6-1 class_7.3-7 gplots_2.11.0.1 >>>>> [13] KernSmooth_2.23-10 caTools_1.14 gdata_2.12.0.2 >>>>> gtools_2.7.1 timecourse_1.32.0 MASS_7.3-26 >>>>> [19] Biobase_2.20.0 BiocGenerics_0.6.0 limma_3.16.5 >>>>> ggplot2_0.9.3.1 BiocInstaller_1.10.1 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] affyio_1.28.0 Biostrings_2.28.0 bit_1.1-10 >>>>> bitops_1.0-5 codetools_0.2-8 colorspace_1.2-2 >>>>> [7] dichromat_2.0-0 digest_0.6.3 ff_2.2-11 >>>>> foreach_1.4.0 GenomicRanges_1.12.4 gtable_0.1.2 >>>>> [13] IRanges_1.18.1 iterators_1.0.6 labeling_0.1 >>>>> marray_1.38.0 munsell_0.4 plyr_1.8 >>>>> [19] preprocessCore_1.22.0 proto_0.3-10 RColorBrewer_1.0-5 >>>>> reshape2_1.2.2 scales_0.2.3 splines_3.0.1 >>>>> [25] stats4_3.0.1 stringr_0.6.2 tkWidgets_1.38.0 >>>>> tools_3.0.1 zlibbioc_1.6.0 >>>>>> >>>>> >>>>> >>>>> -- >>>>> Sent via the guest posting facility at bioconductor.org. >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>
ADD REPLYlink written 6.4 years ago by Johnson, Franklin Theodore140
I'll reply on your initial thread as it seems more appropriate. b 2013/6/20 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: > Dr. Carvalho, > Sorry to get back to you first. > According to previous posts, http://comments.gmane.org/gmane.science .biology.informatics.conductor/35367 > I think it the XYS file error above may be related to the pdInfoBuilder annotation package, pd.pdinfo.gpl11164.ndf.txt. > > I went back to make the build the package again using the XYS file. > I get the [[SIGNAL]] error although PROBE_ID <-> SEQ_ID in the NDF file as per previous email in this thread. > Perhaps this is because XYS is sorted 1,1; 1,2; 2,1; 2,2; 3,1; 3,2....but the NDF is not? > ==================================================================== ================================================== > Building annotation package for Nimblegen Expression Array > NDF: GPL11164.ndf > XYS: 01.xys > ==================================================================== ================================================== > Parsing file: GPL11164.ndf... OK > Parsing file: 01.xys... OK > Merging NDF and XYS files... OK > Preparing contents for featureSet table... OK > Preparing contents for bgfeature table... OK > Preparing contents for pmfeature table... OK > Error in parseNgsPair(object at ndfFile, object at xysFile, verbose = !quiet) : > Control probe possibly identified as Experimental > In addition: Warning message: > In is.na(ndfdata[["SIGNAL"]]) : > is.na() applied to non-(list or vector) of type 'NULL' > > As I take a closer look at the ndf file, I do see control probes in the ndf file that are not present in the merged PAIR-XYS files. These are held in CONTAINER= 'NGS_CONTROLS' with PROBE_ID = XENOSYNTH0040, MISMATCH=10007. > However, !is.na()=TRUE throughout the NDF file. Here is another line representing the CONTROLS: > PROBE_DESIGN_ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA SEQ_ID PROBE_SEQUENCE MISMATCH MATCH_INDEX FEATURE_ID ROW_NUM COL_NUM PROBE_CLASS PROBE_ID POSITION DESIGN_ID X Y > 7552_0712_1000 NGS_CONTROLS EMPTY dark EMPTY N 0 62990761 62990761 1000 712 control EMPTY 0 7552 712 1000 > > I will look at previous threads that may have mentioned just removing these CONTROLS from the NDF file. > In addition to CONTROLS, there are BLOCK1 and RANDOM types as well. These additional two types can be found in the PAIR file. > > Hope to hear from you soon. > Bittersweet! > Franklin > > Great minds discuss ideas. Average minds discuss events. Small minds discuss people. -Eleanor Roosevelt > > ________________________________________ > From: Johnson, Franklin Theodore > Sent: Wednesday, June 19, 2013 11:25 PM > To: Benilton Carvalho > Cc: bioconductor at r-project.org > Subject: RE: FeatureExpressionSet using list.files() in place of read.xysfiles() > > Dr. Carvalho, > Sorry that was my fault. > Yea. I tried that way at first. But got the message below. >> rawData=read.xysfiles(filelist, pkgname="pd.pdinfo.gpl11164.ndf.txt") > All the XYS files must be of the same type. > Error: checkChipTypes(filenames, verbose, "nimblegen") is not TRUE > The logical for check.names is giving the error. > > Perhaps one of my files is incorrect, which I checked and will triple check... > I tried check.names=FALSE as the error seemed to be a logical on the platform type: >> rawData=read.xysfiles(filelist, pkgname="pd.pdinfo.gpl11164.ndf.txt", check.names=F) > Error: These do not exist: > FALSE > > The XYS files did not work either and gave the same result as xys.txt. >> xys.files=list.xysfiles(getwd(), full.names=TRUE) >> xys.files > [1] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/01.xys" > [2] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/02.xys" > [3] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/03.xys" > [4] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/04.xys" > [5] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/05.xys" > [6] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/06.xys" > [7] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/07.xys" > [8] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/08.xys" > [9] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/09.xys" > [10] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/10.xys" > [11] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/11.xys" > [12] "C:/Users/ZHUGRP/Desktop/New folder/XYS.xys files/12.xys" >> basename(xys.files) > [1] "01.xys" "02.xys" "03.xys" "04.xys" "05.xys" "06.xys" "07.xys" "08.xys" "09.xys" "10.xys" "11.xys" "12.xys" >> ripe=read.xysfiles(xys.files, phenoData=pd) > All the XYS files must be of the same type. > Error: checkChipTypes(filenames, verbose, "nimblegen") is not TRUE > > All XYS files are approximately the same size. So, I see no error with making the XYS files. > Given the error, again, it seems like a logical argument on the check.names for the platform type. > What do you think? > Regards, > Franklin > > ________________________________________ > From: Benilton Carvalho [beniltoncarvalho at gmail.com] > Sent: Wednesday, June 19, 2013 8:53 PM > To: Johnson, Franklin Theodore > Cc: bioconductor at r-project.org > Subject: Re: FeatureExpressionSet using list.files() in place of read.xysfiles() > > Dear Franklin, > > I'm not sure I follow your message... my most sincere apologies... > > Now that you have your XYS files, I was expecting you to simply use: > > library(oligo) > rawData = read.xysfiles(filelist, pkgname='pd.pdinfo.gpl11164.ndf.txt') > > doesn't this work for you? (the 'filelist' variable above contains the > names of your converted XYS files) > > Let me know what are your findings... > > b > > 2013/6/19 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: >> Dear Dr. Carvalho, >> >> Thanks for the reply. >> I saw the thread of FAQs how to read in the annotation package made using pdInfoBuilder. >> For anyone having issues, it seems as straight forward as: >> #install pdinfo.gpl11164.ndf.txt >> install.packages("pd.pdinfo.gpl11164.ndf.txt", type="source", repos=NULL) >> Installing package into ?C:/Users/ZHUGRP/Documents/R/win- library/3.0? >> (as ?lib? is unspecified) >> * installing *source* package 'pd.pdinfo.gpl11164.ndf.txt' ... >> ** R >> ** data >> ** inst >> ** preparing package for lazy loading >> ** help >> *** installing help indices >> ** building package indices >> ** testing if installed package can be loaded >> *** arch - i386 >> *** arch - x64 >> * DONE (pd.pdinfo.gpl11164.ndf.txt) >> ################################################################### ######################################### >> I am currently trying to make the FeatureExpressionSet with my converted PAIR -> XYS.txt files unfortunately obtaining X/Y/S only. >> NimbleScan expected .tiff files to read into the software. These files were not available from NCBI/GEO. NimbleGen also did not respond to my inquiry regarding this matter to be able to obtain XYS files from available PAIR files. Using R, I'm testing 12 of 24 tab-delimited XYS files, to also test the annotation package made using pdInfoBuilder. >> #read in files from wd() >> filelist=list.files(pattern=".*.txt") >>> filelist >> [1] "GSM01.txt" "GSM02.txt" "GSM03.txt" "GSM04.txt" "GSM05.txt" "GSM06.txt" "GSM07.txt" "GSM08.txt" "GSM09.txt" "GSM10.txt" "GSM11.txt" "GSM12.txt" >> #read in each data file in filelist as a matrix to make EFS object >>> datalist=lapply(filelist, function(x)as.matrix(read.table(x, header=T, sep="\t", as.is=T))) >> #construct phenoData frame >>> theData=data.frame(Key=rep(c("Week0","Week-2","Week-4"), each=4)) >>> rownames(theData)=basename(filelist) >>> pd=new("AnnotatedDataFrame", data=theData) >> .... >> However, I fail the EFS construction: >> hardline=new("ExpressionFeatureSet", datalist, phenoData=pd, annotation=library(pd.pdinfo.gpl11164.ndf.txt)) >> Error in .names_found_unique(names(value), names(object)) : >> 'sampleNames' replacement list must have unique named elements corresponding to assayData element names >> To confirm, >>> sampleNames(datalist) >> [1] "X" "Y" "PM" >> So, it seems EFS is expecting unique sampleNames for each file in filelist? >> How to read in multiple files into an efs object, as is done with read.xysfiles? Is this doable? >> >> Is it necessary to execute datalist=lapply(filelist, function(x)as.matrix(read.table(x, header=T, sep="\t", as.is=T))) surrounded with Booleans to make the object TRUE, per se? >> i.e. (datalist=lapply(filelist, function(x)as.matrix(read.table(x, header=T, sep="\t", as.is=T))) ) >> Best Regards, >> Franklin >> >> Great minds discuss ideas. Average minds discuss events. Small minds discuss people. -Eleanor Roosevelt >> >> >> >> >> ________________________________________ >> From: Benilton Carvalho [beniltoncarvalho at gmail.com] >> Sent: Thursday, June 13, 2013 4:43 PM >> To: Johnson, Franklin Theodore >> Cc: bioconductor at r-project.org >> Subject: Re: [BioC] PAIR files -- feature set table >> >> dont worry about that particular warning.... just install the package >> and try to read your XYS files. >> >> 2013/6/13 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: >>> Dr. Carvalho, >>> >>> Yes. I see what you mean. >>> Switching the columns helped in the FeatureSet table loading inserted more >>> that 2 rows: >>> >>> Inserting 198661 rows into table featureSet... OK >>> However, the warning message did print again. >>> >>> >>> Warning message: >>> In is.na(ndfdata[["SIGNAL"]]) : >>> is.na() applied to non-(list or vector) of type 'NULL' >>> >>> Below is the output + sessionInfo(), as I upgraded to R 3.0.1. >>> >>> #Begin R command line code: >>> >>>> makePdInfoPackage(arrays, destDir = getwd(), unlink=TRUE) >>> ================================================================== ====================================================================== ====================== >>> >>> >>> Building annotation package for Nimblegen Expression Array >>> NDF: pdinfo_GPL11164.ndf.txt <-new .ndf file with PROBE_ID<->SEQ_ID >>> XYS: XYS.txt >>> ================================================================== ====================================================================== ====================== >>> Parsing file: pdinfo_GPL11164.ndf.txt... OK >>> >>> Parsing file: XYS.txt... OK >>> Merging NDF and XYS files... OK >>> Preparing contents for featureSet table... OK >>> Preparing contents for bgfeature table... OK >>> Preparing contents for pmfeature table... OK >>> Creating package in E:/RANDOM/Test/Yanmin's Microarray Paper/Yanmin >>> Microarray RAW/pd.pdinfo.gpl11164.ndf.txt >>> Inserting 198661 rows into table featureSet... OK >>> Inserting 770599 rows into table pmfeature... OK >>> >>> Counting rows in featureSet >>> Counting rows in pmfeature >>> Creating index idx_pmfsetid on pmfeature... OK >>> Creating index idx_pmfid on pmfeature... OK >>> Creating index idx_fsfsetid on featureSet... OK >>> Saving DataFrame object for PM. >>> Done. >>> Warning message: >>> In is.na(ndfdata[["SIGNAL"]]) : >>> is.na() applied to non-(list or vector) of type 'NULL' >>> >>> >>>> sessionInfo() >>> R version 3.0.1 (2013-05-16) >>> Platform: i386-w64-mingw32/i386 (32-bit) >>> >>> locale: >>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >>> States.1252 LC_MONETARY=English_United States.1252 >>> [4] LC_NUMERIC=C LC_TIME=English_United >>> States.1252 >>> >>> attached base packages: >>> [1] parallel stats graphics grDevices utils datasets methods >>> base >>> >>> other attached packages: >>> [1] pdInfoBuilder_1.24.0 oligo_1.24.0 oligoClasses_1.22.0 >>> affxparser_1.32.1 RSQLite_0.11.4 DBI_0.2-7 >>> Biobase_2.20.0 >>> [8] BiocGenerics_0.6.0 BiocInstaller_1.10.2 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.28.0 Biostrings_2.28.0 bit_1.1-10 >>> codetools_0.2-8 ff_2.2-11 foreach_1.4.1 >>> GenomicRanges_1.12.4 >>> [8] IRanges_1.18.1 iterators_1.0.6 preprocessCore_1.22.0 >>> splines_3.0.1 stats4_3.0.1 tools_3.0.1 >>> zlibbioc_1.6.0 >>> >>> >>> >>>>q() >>> >>> >>> >>> The built pdInfopackage loaded in Destdir is identical to previous message. >>> >>> However the featureSet table now has more than 2 rows... >>> >>> Lastly, I did multiple combos, as my merged file has (X.x, Y.x)<-seems to be >>> identifiers for the 'probe IDs' on the array as well as (X.y, Y.y) <- seems >>> to be the sequence identifiers for the "SEQ_ID". I used X.x, Y.x and PM >>> which gave the result I pasted above. All others had errors. I'm close, but >>> that Warning Message is annoying... >>> >>> >>> >>> Regards, >>> >>> Franklin >>> >>> >>> Great minds discuss ideas. Average minds discuss events. Small minds discuss >>> people. -Eleanor Roosevelt >>> >>> >>> >>> >>> ________________________________________ >>> From: Benilton Carvalho [beniltoncarvalho at gmail.com] >>> Sent: Wednesday, June 12, 2013 8:25 PM >>> >>> To: Johnson, Franklin Theodore >>> Cc: bioconductor at r-project.org >>> Subject: Re: [BioC] PAIR files -- feature set table >>> >>> That does not look ok. >>> >>> The problem is the count for the featureSet table... This table stores >>> the information for "genes" (or whatever the target for this >>> particular array is)... so, it is unlikely that you have a microarray >>> with only 2 "target units"... I'd expect something around the >>> thousands... >>> >>> pdInfoBuilder uses the information in SEQ_ID (in the NDF) to get the >>> target information (i.e., the contents for featureSet). >>> >>> Given that this is a custom array, I believe that the best idea is to >>> contact the person who designed it and ask more details about the >>> design (in particular, how many probesets and average number of probes >>> per probeset)... >>> >>> I've seen some designs in which the information that was expected to >>> be in SEQ_ID was actually stored in PROBE_ID (in such cases, the user >>> needs to create a backup copy of the NDF, and then move the contents >>> of PROBE_ID to SEQ_ID - and vice-versa). >>> >>> b >>> >>> 2013/6/12 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: >>>> Dear Dr. Carvalho, >>>> >>>> Recently, we had cooresponence regaring makePDInfoPackage for an NimbleGen >>>> apple microarray. >>>> I was able to merge the ndf design and XYS files using PROBE_ID. >>>> As a reminder this is a custom array, and there are no SIGNAL==NAs for >>>> control probes. >>>> It seemed to work: >>>>> makePdInfoPackage(seed, destDir("")) >>>> >>>> ================================================================= ====================================================================== ===================== >>>> Building annotation package for Nimblegen Expression Array >>>> NDF: GPL11164.ndf >>>> XYS: XYS.txt >>>> >>>> ================================================================= ====================================================================== ===================== >>>> Parsing file: GPL11164.ndf... OK >>>> Parsing file: XYS.txt... OK >>>> Merging NDF and XYS files... OK >>>> Preparing contents for featureSet table... OK >>>> Preparing contents for bgfeature table... OK >>>> Preparing contents for pmfeature table... OK >>>> Creating package in >>>> C:/Users/franklin.johnson.PW50-WEN/Desktop/Test/Yanmin's Microarray >>>> Paper/Yanmin Microarray RAW/pd.gpl11164 >>>> Inserting 2 rows into table featureSet... OK >>>> Inserting 765524 rows into table pmfeature... OK >>>> Inserting 5075 rows into table bgfeature... OK >>>> Counting rows in bgfeature >>>> Counting rows in featureSet >>>> Counting rows in pmfeature >>>> Creating index idx_bgfsetid on bgfeature... OK >>>> Creating index idx_bgfid on bgfeature... OK >>>> Creating index idx_pmfsetid on pmfeature... OK >>>> Creating index idx_pmfid on pmfeature... OK >>>> Creating index idx_fsfsetid on featureSet... OK >>>> Saving DataFrame object for PM. >>>> Saving DataFrame object for BG. >>>> Done. >>>> Warning message: >>>> In is.na(ndfdata[["SIGNAL"]]) : >>>> is.na() applied to non-(list or vector) of type 'NULL' >>>>> >>>> >>>> In contrast to this warning message, I see a pdinfopackage directory with >>>> 4 subdirectories: c=("data", "inst", "man", R"), as well as >>>> subsubdirectories in "inst"=c("extdata", and "Unit Tests"), in addition to >>>> two text files in the main directory: c=("DESCRIPTION", "NAMESPACE") were >>>> created in my destination folder. >>>> Before using "oligo", if possible, I wanted to confirm with you that this >>>> package is viable to use with "oligo" although a warning message that may >>>> not pertain to my custom designed microarray was printed. >>>> >>>> Regards, >>>> Franklin >>>> >>>> Great minds discuss ideas. Average minds discuss events. Small minds >>>> discuss people. -Eleanor Roosevelt >>>> >>>> >>>> >>>> >>>> ________________________________________ >>>> From: Johnson, Franklin Theodore >>>> Sent: Friday, June 07, 2013 10:39 AM >>>> To: Benilton Carvalho >>>> Cc: bioconductor at r-project.org >>>> Subject: RE: [BioC] PAIR files -- feature set table >>>> >>>> Resending to bioconductor message thread: >>>> >>>> Dear Dr. Carvalho, >>>> Thanks for the response. >>>> As you suggested, I will look into the merge function using "Probe_ID". >>>> After reading in the data, I will start here: merge.datasets(dataset1, >>>> dataset2, by="key"). >>>> Best Regards, >>>> Franklin >>>> >>>> Great minds discuss ideas. Average minds discuss events. Small minds >>>> discuss people. -Eleanor Roosevelt >>>> >>>> ________________________________________ >>>> From: Benilton Carvalho [beniltoncarvalho at gmail.com] >>>> Sent: Thursday, June 06, 2013 8:11 PM >>>> To: Johnson, Franklin Theodore >>>> Cc: bioconductor at r-project.org; franklin.johnson at wsu.edu >>>> Subject: Re: [BioC] PAIR files -- feature set table >>>> >>>> You will need to merge the PAIR and the NDF using the PROBE_ID column >>>> as key. This will allow you to get the X/Y coordinates needed to >>>> create the XYS as described on the other messages. >>>> >>>> Regarding annotation, you may need to contact NimbleGen to request >>>> this information directly from them... >>>> >>>> benilton >>>> >>>> 2013/6/6 Johnson, Franklin Theodore <franklin.johnson at="" email.wsu.edu="">: >>>>> Dear Dr. Carvalho, >>>>> >>>>> Muchos grasias for the reply. >>>>> >>>>> Actually, this is what my .ndf file looks like: >>>>>> head(ndf) >>>>> PROBE_DESIGN_ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA SEQ_ID >>>>> 1 7552_0343_0009 Duplicate_1 >>>>> 2 7552_0345_0009 Duplicate_2 >>>>> 3 7552_0347_0009 Duplicate_1 >>>>> 4 7552_0349_0009 Duplicate_2 >>>>> 5 7552_0351_0009 Duplicate_2 >>>>> 6 7552_0353_0009 Duplicate_1 >>>>> PROBE_SEQUENCE MISMATCH >>>>> MATCH_INDEX FEATURE_ID ROW_NUM COL_NUM PROBE_CLASS >>>>> 1 cttgactcttctaagttcaaaggtaactcaagtgaagctgtcagatatgatccttcca 0 >>>>> 64535488 64535488 9 343 >>>>> 2 cccaagcattaaaccttactcatatacttataatgcagccatcaagagtttgtgcaagg 0 >>>>> 64799310 64799310 9 345 >>>>> 3 agggaggctgaaagagagagtgaatggtccagctgggcataattgctgca 0 >>>>> 64476989 64476989 9 347 >>>>> 4 ttgttggtgggggtgttgcccttagtaccccagaccttgaagcagttaaa 0 >>>>> 64862794 64862794 9 349 >>>>> 5 gtgtggggccccctttctttaactggaacctttctttgaagcaatttggg 0 >>>>> 64832726 64832726 9 351 >>>>> 6 ttgtccaattccaacatgccgagacggcagggattgtgatcgtgttgttc 0 >>>>> 64435686 64435686 9 353 >>>>> PROBE_ID POSITION DESIGN_ID X Y >>>>> 1 Contig19819_1_f_28_10_535 0 7552 343 9 >>>>> 2 Malus_CN899188_2_f_147_1_755 0 7552 345 9 >>>>> 3 Contig20738_8_r_1179_2_1432 0 7552 347 9 >>>>> 4 Malus_CN880097_2_r_336_2_536 0 7552 349 9 >>>>> 5 Malus_CN918117_2_f_632_1_781 0 7552 351 9 >>>>> 6 Contig1991_1_f_71_2_1239 0 7552 353 9 >>>>> >>>>> The pair files, .532 pair files only (one-color arrays), only obtain the >>>>> probe ID and signal; after some text at the top describing the experiment. >>>>> My real issue is that I can further normalize and analyze the RMA files with >>>>> sva and limma, etc. However, I cannot annotate the probes without the array >>>>> annotation, as there are duplicates in the ndf file which are removed in the >>>>> RMA.pair files available on NCBI/GEO. So they will not match in any >>>>> annotation package I've failed at trying. >>>>> So, I' tried to go back and start from the raw pair files...this custom >>>>> array is really a "custom" array without >>>>> NimbleScan. >>>>> >>>>> Salud, >>>>> Franklin >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> Great minds discuss ideas. Average minds discuss events. Small minds >>>>> discuss people. -Eleanor Roosevelt >>>>> >>>>> >>>>> >>>>> >>>>> ________________________________________ >>>>> From: Benilton Carvalho [beniltoncarvalho at gmail.com] >>>>> Sent: Wednesday, June 05, 2013 6:42 PM >>>>> To: FRANKLIN JOHNSON [guest] >>>>> Cc: bioconductor at r-project.org; franklin.johnson at wsu.edu; pdInfoBuilder >>>>> Maintainer >>>>> Subject: Re: [BioC] PAIR files -- feature set table >>>>> >>>>> It's an unfortunate mistake to have the pairFile *argument* in the >>>>> call (not in the slots session, but I see your point). :-( I'll make >>>>> sure that this is fixed. >>>>> >>>>> You need to convert the PAIR files to XYS... >>>>> >>>>> Some refs that should help you in the process: >>>>> >>>>> https://stat.ethz.ch/pipermail/bioconductor/2012-January/043186.html >>>>> >>>>> http://comments.gmane.org/gmane.science.biology.informatics.cond uctor/27547 >>>>> >>>>> b >>>>> >>>>> 2013/6/5 FRANKLIN JOHNSON [guest] <guest at="" bioconductor.org="">: >>>>>> >>>>>> Dear Maintainer, >>>>>> >>>>>> I downloaded available NimbleGen 'single channel' 532.PAIR files for a >>>>>> custom built expression microarray from NCBI/GEO (GPL11164). However, I get >>>>>> an error message when I try to make the annotation for this platform using >>>>>> pdInfoBuild. >>>>>> >>>>>> In pdInfoBuilder Reference Manual (June 5, 2013), under the >>>>>> NgsExpressionPDInfoPkgSeed method, there is a slot for pairFile, although, >>>>>> showClasses("Ngs.."), does not show a slot for this, only, XYS. Thus, I >>>>>> changed the .pair file extension to .xys. >>>>>> >>>>>> (ndf<- list.files(getwd(), pattern=".ndf", full.names=TRUE)) # read >>>>>> annotation file >>>>>> [1] "C:/Users/franklin.johnson.PW99-WEN/Desktop/Test/Yanmin's Microarray >>>>>> Paper/Yanmin Microarray RAW/GPL11164.ndf" >>>>>> >>>>>> (xys <- list.files(getwd(), pattern = ".xys", full.names = TRUE)[1]) >>>>>> [1] "C:/Users/franklin.johnson.PW99-WEN/Desktop/Test/Yanmin's Microarray >>>>>> Paper/Yanmin Microarray RAW/GSM618107_14418002_532.xys" >>>>>> >>>>>> But, doing this resulted in an error message: >>>>>> seed <- new("NgsExpressionPDInfoPkgSeed", ndfFile = ndf, xysFile = xys, >>>>>> author = "FJ", organism = "Apple", species = "Malus x Domestica cv.GD") >>>>>> >>>>>> makePdInfoPackage(arrays, destDir = getwd()) >>>>>> >>>>>> =============================================================== ====================================================================== ======= >>>>>> Building annotation package for Nimblegen Expression Array >>>>>> NDF: GPL11164.ndf >>>>>> XYS: GSM618107_14418002_532.xys >>>>>> >>>>>> =============================================================== ====================================================================== ======= >>>>>> Parsing file: GPL11164.ndf... OK >>>>>> Parsing file: GSM618107_14418002_532.xys... OK >>>>>> Merging NDF and XYS files... OK >>>>>> Preparing contents for featureSet table... Error in >>>>>> `[.data.frame`(ndfdata, , colsFS) : undefined columns selected >>>>>> In addition: Warning message: >>>>>> In is.na(ndfdata[["SIGNAL"]]) : >>>>>> is.na() applied to non-(list or vector) of type 'NULL' >>>>>> >>>>>> The only files available from NCBI/GEO are 24 PAIR files and 1 ndf. It >>>>>> seems .xys has a different arrangement than .pair, thus .ndf is not >>>>>> applicable to annotate the .pair file? Any suggestions? >>>>>> Hope to hear from you soon. >>>>>> Franklin >>>>>> >>>>>> -- output of sessionInfo(): >>>>>> >>>>>>> sessionInfo() >>>>>> R version 3.0.1 (2013-05-16) >>>>>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>>>>> >>>>>> locale: >>>>>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >>>>>> States.1252 LC_MONETARY=English_United States.1252 >>>>>> [4] LC_NUMERIC=C LC_TIME=English_United >>>>>> States.1252 >>>>>> >>>>>> attached base packages: >>>>>> [1] tcltk grid parallel stats graphics grDevices utils >>>>>> datasets methods base >>>>>> >>>>>> other attached packages: >>>>>> [1] pdInfoBuilder_1.24.0 oligo_1.24.0 oligoClasses_1.22.0 >>>>>> affxparser_1.32.1 RSQLite_0.11.4 DBI_0.2-7 >>>>>> [7] Mfuzz_2.18.0 DynDoc_1.38.0 widgetTools_1.38.0 >>>>>> e1071_1.6-1 class_7.3-7 gplots_2.11.0.1 >>>>>> [13] KernSmooth_2.23-10 caTools_1.14 gdata_2.12.0.2 >>>>>> gtools_2.7.1 timecourse_1.32.0 MASS_7.3-26 >>>>>> [19] Biobase_2.20.0 BiocGenerics_0.6.0 limma_3.16.5 >>>>>> ggplot2_0.9.3.1 BiocInstaller_1.10.1 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> [1] affyio_1.28.0 Biostrings_2.28.0 bit_1.1-10 >>>>>> bitops_1.0-5 codetools_0.2-8 colorspace_1.2-2 >>>>>> [7] dichromat_2.0-0 digest_0.6.3 ff_2.2-11 >>>>>> foreach_1.4.0 GenomicRanges_1.12.4 gtable_0.1.2 >>>>>> [13] IRanges_1.18.1 iterators_1.0.6 labeling_0.1 >>>>>> marray_1.38.0 munsell_0.4 plyr_1.8 >>>>>> [19] preprocessCore_1.22.0 proto_0.3-10 RColorBrewer_1.0-5 >>>>>> reshape2_1.2.2 scales_0.2.3 splines_3.0.1 >>>>>> [25] stats4_3.0.1 stringr_0.6.2 tkWidgets_1.38.0 >>>>>> tools_3.0.1 zlibbioc_1.6.0 >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Sent via the guest posting facility at bioconductor.org. >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at r-project.org >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>
ADD REPLYlink written 6.4 years ago by Benilton Carvalho4.3k
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