Question: Error: Re: Annotation Database for Agilent 8x60K Human Gene Expression Arrays
0
gravatar for Karthik K N
7.1 years ago by
Karthik K N200
Karthik K N200 wrote:
Hello Marc, I am trying to create an annotation package for Agilent 8x60K human gene expression array using SQLForge. I have a agilent_ID.txt file with Agilent Probe IDs in the first column and Entrez Gene IDs in the second column. I am using the following code: >library("human.db0") >agilent_IDs = system.file("extdata", "agilent_ID.txt", package="human.db0") >myMeta = c("DBSCHEMA"="HUMANCHIP_DB", "ORGANISM"="Homo sapiens", "SPECIES"="Human", "MANUFACTURER"="Agilent", "CHIPNAME"="Human whole genome 8x60k Array ", "MANUFACTURERURL"="http://www.chem.agilent.com") >tmpout = tempdir() >available.chipdbschemas() >populateDB("HUMANCHIP_DB", affy = FALSE, prefix = "Agilent 8x60K", fileName = agilent_IDs, metaDataSrc = myMeta, baseMapType = "eg", outputDir = tmpout) >seed <- new("AnnDbPkgSeed", Package = "Agilent 8x60K.db", Version = "1.0.0", PkgTemplate = "HUMANCHIP.DB", AnnObjPrefix = "Agilent 8x60K") >makeAnnDbPkg(seed, file.path(tmpout, "Agilent 8x60K.sqlite"), dest_dir = tmpout) simplifying probes table dropping redundant data Creating package in C:\Users\1288\AppData\Local\Temp\Rtmp6JV7Qu/Agilent 8x60K.db *Then, when I try to install the package using the code given below:* >install.packages("C:/Users/1288/AppData/Local/Temp/Rtmp6JV7Qu/Agilent 8x60K.db", repos=NULL, type="source") *I am getting the error shown below:* * * Installing package(s) into ‘C:/Users/1288/Documents/R/win- library/2.15’ (as ‘lib’ is unspecified) * installing *source* package 'Agilent 8x60K.db' ... Error : Invalid DESCRIPTION file Malformed package name See the information on DESCRIPTION files in section 'Creating R packages' of the 'Writing R Extensions' manual. ERROR: installing package DESCRIPTION failed for package 'Agilent 8x60K.db' * removing 'C:/Users/kalash1288/Documents/R/win-library/2.15/Agilent 8x60K.db' Warning messages: 1: running command 'C:/PROGRA~1/R/R-215~1.0/bin/x64/R CMD INSTALL -l "C:/Users/1288/Documents/R/win-library/2.15" "C:/Users/1288/AppData/Local/Temp/RTMP6J~1/Agilent 8x60K.db"' had status 1 2: In install.packages("C:/Users/1288/AppData/Local/Temp/Rtmp6JV7Qu/Agilent 8x60K.db", : installation of package ‘C:/Users/1288/AppData/Local/Temp/RTMP6J~1/Agilent 8x60K.db’ had non- zero exit status Can you please help me solve this problem? Where am I making a mistake? I am also providing the session info below. Thanks a lot for your help. Regards, Karthik -------------------------------- *Session Info* R version 2.15.0 (2012-03-30) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252 [3] LC_MONETARY=English_India.1252 LC_NUMERIC=C [5] LC_TIME=English_India.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RSQLite_0.11.1 DBI_0.2-5 AnnotationDbi_1.18.1 [4] Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] IRanges_1.14.4 limma_3.12.1 limmaGUI_1.32.0 stats4_2.15.0 [5] tcltk_2.15.0 tools_2.15.0 > > ---------- Forwarded message ---------- > From: Marc Carlson <mcarlson@fhcrc.org> > Date: Wed, Jun 20, 2012 at 12:28 AM > Subject: Re: [BioC] Annotation Database for Agilent 8x60K Human Gene > Expression Arrays > To: bioconductor@r-project.org > > > Hi Karthik, > > The 8x60 arrays have a different design ID so out of caution, I would not > recommend that you use that package for this. Even if all the IDs from the > other design id are present here (and that is a big if), you may still in > certain circumstances end up thinking that you tried to measure a bunch of > things that you did not try to measure. The design ID was put into the > name to try and avoid this confusion and to warn you about possible > inconsistencies. > > Here is the page from Agilents website that gives the design IDs for the > platforms in question along with links to their eArray web application that > allows access to the files which they supply probe mappings for. > > http://www.genomics.agilent.**com/CollectionSubpage.aspx?** > PageType=Product&SubPageType=**ProductData&PageID=1516<http: www.ge="" nomics.agilent.com="" collectionsubpage.aspx?pagetype="Product&amp;SubPageType" =productdata&pageid="1516"> > > From that eArray link you should be able to just download the file (one > for the 8x60 arrays) and then just follow the directions from the SQLForge > vignette from the AnnotationDbi package to make an annotation package for > the 8x60 arrays. It's pretty easy to make an annotation package. The > tricky part is usually getting the mapping information from the > manufacturers, but it sounds like you have already done that part. > > Here is where you can find that SQLForge vignette: > > http://www.bioconductor.org/**packages/2.10/bioc/vignettes/** > AnnotationDbi/inst/doc/**SQLForge.pdf<http: www.bioconductor.org="" pa="" ckages="" 2.10="" bioc="" vignettes="" annotationdbi="" inst="" doc="" sqlforge.pdf=""> > > > For more information about the Agi4x44PreProcess you should look at the > vignette for that package here: > > http://www.bioconductor.org/**packages/2.10/bioc/vignettes/** > Agi4x44PreProcess/inst/doc/**Agi4x44PreProcess.pdf<http: www.biocon="" ductor.org="" packages="" 2.10="" bioc="" vignettes="" agi4x44preprocess="" inst="" doc="" agi="" 4x44preprocess.pdf=""> > > The vignette certainly makes it seem like you can use this package with > other Agilent annotations, but you might want to ask Pedro about exactly > how accommodating his design is intended to be. > > Hope this helps, > > > Marc > > > > > On 06/18/2012 04:09 AM, Karthik K N wrote: > >> Dear Members (and especially Marc Carlson), >> >> I have few questions: >> >> 1. I was wondering whether HsAgilentDesign026652.db is the latest updated >> database for Agilent 8x60K human gene expression arrays or is there any >> other file? I have been told by Axel that HsAgilentDesign026652.db cover >> the oligos used by the Agilent 4x44Kv2 arrays, so I am not sure if I can >> use this for 8x60K arrays. >> >> 2. If I can indeed use HsAgilentDesign026652.db for 8x60K arrays, is it >> possible to use it as annotation file for Agi4x44PreProcess package so >> that >> I can use the same codes from this package to analyze 8x60K arrays? >> >> 3. If I want to create an annotation file to be used in any of the >> packages, what are the requirements (files, tools etc) for it? I have an >> annotation file in excel format given to me by my microarray service >> provider, so If I want to use that annotation file in Agi4x44Preprocess >> package (or any other package that requires this file) what should I do? >> >> Thanks a lot in advance for all your suggestions! >> >> Cheers, >> >> Karthik >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > > > [[alternative HTML version deleted]]
ADD COMMENTlink modified 7.1 years ago by Marc Carlson7.2k • written 7.1 years ago by Karthik K N200
Answer: Error: Re: Annotation Database for Agilent 8x60K Human Gene Expression Arrays
0
gravatar for Marc Carlson
7.1 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi Karthik, As you discovered, R won't allow you to put spaces into a package name like that. Create the package again, but this time when you pass the argument for prefix (this is what becomes the package name) don't put any spaces in that string. Also, you should not have to do all those steps (populateDB, seed, makeAnnDbPkg). You should be able to just call makeDBPackage() as described later on the vignette to make the package. Please let me know if you have any further troubles. Marc On 07/03/2012 11:37 PM, Karthik K N wrote: > > Hello Marc, > > I am trying to create an annotation package for Agilent 8x60K human > gene expression array using SQLForge. I have a agilent_ID.txt file > with Agilent Probe IDs in the first column and Entrez Gene IDs in the > second column. I am using the following code: > > > >library("human.db0") > > >agilent_IDs = system.file("extdata", "agilent_ID.txt", > package="human.db0") > > >myMeta = c("DBSCHEMA"="HUMANCHIP_DB", "ORGANISM"="Homo sapiens", > "SPECIES"="Human", "MANUFACTURER"="Agilent", "CHIPNAME"="Human whole > genome 8x60k Array ", "MANUFACTURERURL"="http://www.chem.agilent.com") > > >tmpout = tempdir() > > >available.chipdbschemas() > > >populateDB("HUMANCHIP_DB", affy = FALSE, prefix = "Agilent 8x60K", > fileName = agilent_IDs, metaDataSrc = myMeta, baseMapType = "eg", > outputDir = tmpout) > > >seed <- new("AnnDbPkgSeed", Package = "Agilent 8x60K.db", Version = > "1.0.0", PkgTemplate = "HUMANCHIP.DB", AnnObjPrefix = "Agilent 8x60K") > > >makeAnnDbPkg(seed, file.path(tmpout, "Agilent 8x60K.sqlite"), > dest_dir = tmpout) > > simplifying probes table > dropping redundant data > Creating package in > C:\Users\1288\AppData\Local\Temp\Rtmp6JV7Qu/Agilent 8x60K.db > > *Then, when I try to install the package using the code given below:* > > >install.packages("C:/Users/1288/AppData/Local/Temp/Rtmp6JV7Qu/Agilent > 8x60K.db", repos=NULL, type="source") > > *I am getting the error shown below:* > * > * > Installing package(s) into ‘C:/Users/1288/Documents/R/win- library/2.15’ > (as ‘lib’ is unspecified) > * installing *source* package 'Agilent 8x60K.db' ... > Error : Invalid DESCRIPTION file > > Malformed package name > > See the information on DESCRIPTION files in section 'Creating R > packages' of the 'Writing R Extensions' manual. > > ERROR: installing package DESCRIPTION failed for package 'Agilent > 8x60K.db' > * removing 'C:/Users/kalash1288/Documents/R/win-library/2.15/Agilent > 8x60K.db' > Warning messages: > 1: running command 'C:/PROGRA~1/R/R-215~1.0/bin/x64/R CMD INSTALL -l > "C:/Users/1288/Documents/R/win-library/2.15" > "C:/Users/1288/AppData/Local/Temp/RTMP6J~1/Agilent 8x60K.db"' had > status 1 > 2: In > install.packages("C:/Users/1288/AppData/Local/Temp/Rtmp6JV7Qu/Agilent > 8x60K.db", : > installation of package > ‘C:/Users/1288/AppData/Local/Temp/RTMP6J~1/Agilent 8x60K.db’ had > non-zero exit status > > Can you please help me solve this problem? Where am I making a mistake? > > I am also providing the session info below. > > Thanks a lot for your help. > > Regards, > > Karthik > > -------------------------------- > > */Session Info /* > > R version 2.15.0 (2012-03-30) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252 > [3] LC_MONETARY=English_India.1252 LC_NUMERIC=C > [5] LC_TIME=English_India.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] RSQLite_0.11.1 DBI_0.2-5 AnnotationDbi_1.18.1 > [4] Biobase_2.16.0 BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] IRanges_1.14.4 limma_3.12.1 limmaGUI_1.32.0 stats4_2.15.0 > [5] tcltk_2.15.0 tools_2.15.0 > > > > > ---------- Forwarded message ---------- > From: *Marc Carlson* <mcarlson@fhcrc.org <mailto:mcarlson@fhcrc.org="">> > Date: Wed, Jun 20, 2012 at 12:28 AM > Subject: Re: [BioC] Annotation Database for Agilent 8x60K Human > Gene Expression Arrays > To: bioconductor@r-project.org <mailto:bioconductor@r-project.org> > > > Hi Karthik, > > The 8x60 arrays have a different design ID so out of caution, I > would not recommend that you use that package for this. Even if > all the IDs from the other design id are present here (and that is > a big if), you may still in certain circumstances end up thinking > that you tried to measure a bunch of things that you did not try > to measure. The design ID was put into the name to try and avoid > this confusion and to warn you about possible inconsistencies. > > Here is the page from Agilents website that gives the design IDs > for the platforms in question along with links to their eArray web > application that allows access to the files which they supply > probe mappings for. > > http://www.genomics.agilent. com/CollectionSubpage.aspx? > PageType=Product&SubPageType= ProductData&PageID=1516 > <http: www.genomics.agilent.com="" collectionsubpage.aspx?pagetype="Product&amp;SubPageType=ProductData&amp;PageID=1516"> > > From that eArray link you should be able to just download the file > (one for the 8x60 arrays) and then just follow the directions from > the SQLForge vignette from the AnnotationDbi package to make an > annotation package for the 8x60 arrays. It's pretty easy to make > an annotation package. The tricky part is usually getting the > mapping information from the manufacturers, but it sounds like you > have already done that part. > > Here is where you can find that SQLForge vignette: > > http://www.bioconductor.org/ packages/2.10/bioc/vignettes/ > AnnotationDbi/inst/doc/ SQLForge.pdf > <http: www.bioconductor.org="" packages="" 2.10="" bioc="" vignettes="" annota="" tiondbi="" inst="" doc="" sqlforge.pdf=""> > > > For more information about the Agi4x44PreProcess you should look > at the vignette for that package here: > > http://www.bioconductor.org/ packages/2.10/bioc/vignettes/ > Agi4x44PreProcess/inst/doc/ Agi4x44PreProcess.pdf > <http: www.bioconductor.org="" packages="" 2.10="" bioc="" vignettes="" agi4x4="" 4preprocess="" inst="" doc="" agi4x44preprocess.pdf=""> > > The vignette certainly makes it seem like you can use this package > with other Agilent annotations, but you might want to ask Pedro > about exactly how accommodating his design is intended to be. > > Hope this helps, > > > Marc > > > > > On 06/18/2012 04:09 AM, Karthik K N wrote: > > Dear Members (and especially Marc Carlson), > > I have few questions: > > 1. I was wondering whether HsAgilentDesign026652.db is the > latest updated > database for Agilent 8x60K human gene expression arrays or is > there any > other file? I have been told by Axel that > HsAgilentDesign026652.db cover > the oligos used by the Agilent 4x44Kv2 arrays, so I am not > sure if I can > use this for 8x60K arrays. > > 2. If I can indeed use HsAgilentDesign026652.db for 8x60K > arrays, is it > possible to use it as annotation file for Agi4x44PreProcess > package so that > I can use the same codes from this package to analyze 8x60K > arrays? > > 3. If I want to create an annotation file to be used in any of the > packages, what are the requirements (files, tools etc) for it? > I have an > annotation file in excel format given to me by my microarray > service > provider, so If I want to use that annotation file in > Agi4x44Preprocess > package (or any other package that requires this file) what > should I do? > > Thanks a lot in advance for all your suggestions! > > Cheers, > > Karthik > > [[alternative HTML version deleted]] > > ______________________________ _________________ > Bioconductor mailing list > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > https://stat.ethz.ch/mailman/ listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane. > science.biology.informatics. conductor > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > ______________________________ _________________ > Bioconductor mailing list > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > https://stat.ethz.ch/mailman/ listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane. > science.biology.informatics. conductor > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > [[alternative HTML version deleted]]
ADD COMMENTlink written 7.1 years ago by Marc Carlson7.2k
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