Question: questions about altcdfenv
0
gravatar for Hui-Yi Chu
10.6 years ago by
Hui-Yi Chu160
Hui-Yi Chu160 wrote:
Hi, I am using Affymetrix yeast2 array so that I wanna get rid of S. pombe gene expression value before further analysis. Earlier I was using filtration function to filter out the lowest signals which I assumed from S. pombe. However, this method seems not perfect since I got the result. Thus, I turned to use altcdfenv package to create a S.C. only env. But I got some errors when I applied this env for next analysis. I really appreciate your help!!! Here is the code: ## data importing library("affy") library("limma") targets <- readTargets("fed_total.txt") raw.data <- ReadAffy(filenames = targets $ filename) ## create altcdfenv library(altcdfenvs) getCdfEnvAffy(raw.data); library(yeast2cdf) twocdf <- wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf"); print(twocdf) sc.ids <- scan("sc_IDs.txt", what="") ### got 5749 s.c. ids sc.only.cdf <- twocdf[sc.ids] sc.only.cdf @ envName <- "S_cerevisiae_IDs Only"; print(sc.only.cdf) ### apply this subset-cdf to "affybatch" env.sc.cdf <- as(sc.only.cdf, "environment") raw.data @cdfName <- "sc.only.cdf" save(raw.data, sc.only.cdf, env.sc.cdf, file="sc_only_cdf.rda") ### start further analysis eset <- rma(aaa) ----- got errors: Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : invalid object for 'as.environment' ### tried pa calls--- also got errors eset.pm <- mas5calls(raw.data) Getting probe level data... Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : invalid object for 'as.environment' Error in as.matrix(pm(object)) : error in evaluating the argument 'x' in selecting a method for function 'as.matrix' If there is any mistake in my codes???? Any suggestions are appreciated! Many thanks! Hui-Yi > sessionInfo() R version 2.7.2 (2008-08-25) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] altcdfenvs_2.2.0 hypergraph_1.12.0 Biostrings_2.8.18 [4] makecdfenv_1.18.0 scatterplot3d_0.3-27 yeast2.db_2.2.0 [7] affycoretools_1.12.1 annaffy_1.12.1 KEGG.db_2.2.0 [10] gcrma_2.12.1 matchprobes_1.12.1 biomaRt_1.14.1 [13] RCurl_0.9-3 GOstats_2.6.0 Category_2.6.0 [16] RBGL_1.16.0 annotate_1.18.0 xtable_1.5-3 [19] GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.7-0 [22] DBI_0.2-4 graph_1.18.1 gplots_2.6.0 [25] gdata_2.4.2 gtools_2.5.0 Heatplus_1.10.0 [28] RColorBrewer_1.0-2 genefilter_1.20.0 survival_2.34-1 [31] yeast2cdf_2.2.0 limma_2.14.6 affy_1.18.2 [34] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 loaded via a namespace (and not attached): [1] cluster_1.11.11 XML_1.94-0.1 [[alternative HTML version deleted]]
go yeast2 cdf probe • 615 views
ADD COMMENTlink modified 10.6 years ago by Jenny Drnevich1.9k • written 10.6 years ago by Hui-Yi Chu160
Answer: questions about altcdfenv
0
gravatar for Hui-Yi Chu
10.6 years ago by
Hui-Yi Chu160
Hui-Yi Chu160 wrote:
Dear BioC list, Before turning to use altcdfenv package, I used genefilter package to generate a "filtered" expressionSet, but after filtration and annotation, it still contained lots of blank gene symbols. Some of those probesets without symbols are from S.Pombe, so that is the reason going back to use altcdfenvs. Furthermore, I have checked the annotated+expression value table (before filtration, total=10928 probesets), it has abnormally high numbers of NA gene names--- 4707...I checked ORF as well, which gave me 5222 blank ORFs.... Please, can anybody give me any idea that how can I deal with this issue?? Many many thanks!!! Best, Hui-Yi *Codes*: ## data importing > library("affy") > library("limma") > targets <- readTargets("fed_total.txt") > aaa <- ReadAffy(filenames = targets $ filename) > eset <- rma(aaa) > #### add annotation info and output as a table > library("annotata") > library("yeast2.db") > annotation(eset) <- "yeast2.db" > #skip following codes for creating a data frame for exporting to excel... ### filtration library("genefilter") f1 <- anyNA f2 <- pOverA(0.25, log2(100)) ff <- filterfun(f1, f2) selected <- genefilter(eset, ff) esetsub <- eset[selected,] ## limma fit and contrast library("limma") design <- model.matrix(~0+factor(c(1,1,2,2,3,3))) colnames(design) <- c("wt", "mut.a","mut.b") fit <- lmFit(exprs(esetsub), design) fit2 <- eBayes(fit) contrast.matrix <- makeContrasts("mut.a vs wt" = mut.a-wt, "mut.b vs wt" = mut.b-wt,levels=design) #skip following codes for DEG analysis [[alternative HTML version deleted]]
ADD COMMENTlink written 10.6 years ago by Hui-Yi Chu160
Hi Hui-Yi, Without specific examples I can only guess, but I am betting that the trouble you are having is related to two facts: 1) approximately half of the probesets on the yeast2 affymetrix platform are from S.pombe. (the other half are from S.cerevisiae) and 2) the annotation packages that we have made for yeast platforms are based on SGD, which is important since SGD does not have annotations for S.pombe. If you know about some great sources of annotations for S.pombe, I would love to know more about them. Marc Hui-Yi Chu wrote: > Dear BioC list, > > Before turning to use altcdfenv package, I used genefilter package to > generate a "filtered" expressionSet, but after filtration and annotation, it > still contained lots of blank gene symbols. Some of those probesets without > symbols are from S.Pombe, so that is the reason going back to use > altcdfenvs. Furthermore, I have checked the annotated+expression value table > (before filtration, total=10928 probesets), it has abnormally high numbers > of NA gene names--- 4707...I checked ORF as well, which gave me 5222 blank > ORFs.... > Please, can anybody give me any idea that how can I deal with this issue?? > Many many thanks!!! > > Best, > Hui-Yi > > > *Codes*: > ## data importing > > >> library("affy") >> library("limma") >> targets <- readTargets("fed_total.txt") >> aaa <- ReadAffy(filenames = targets $ filename) >> eset <- rma(aaa) >> >> > > #### add annotation info and output as a table > > >> library("annotata") >> library("yeast2.db") >> annotation(eset) <- "yeast2.db" >> >> > #skip following codes for creating a data frame for exporting > to excel... > > ### filtration > library("genefilter") > f1 <- anyNA > f2 <- pOverA(0.25, log2(100)) > ff <- filterfun(f1, f2) > selected <- genefilter(eset, ff) > esetsub <- eset[selected,] > > ## limma fit and contrast > library("limma") > design <- model.matrix(~0+factor(c(1,1,2,2,3,3))) > colnames(design) <- c("wt", "mut.a","mut.b") > fit <- lmFit(exprs(esetsub), design) > fit2 <- eBayes(fit) > contrast.matrix <- makeContrasts("mut.a vs wt" = mut.a-wt, > "mut.b vs wt" = mut.b-wt,levels=design) > #skip following codes for DEG analysis > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD REPLYlink written 10.6 years ago by Marc Carlson7.2k
Answer: questions about altcdfenv
0
gravatar for Jenny Drnevich
10.6 years ago by
Jenny Drnevich1.9k
United States
Jenny Drnevich1.9k wrote:
Hi Hui-Yi, See this recent post about another way to remove probe sets: https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html This will temporarily remove the probe sets from the regular yeast2cdf, and it's much easier to use than atlcdfenvs if you only want to remove particular probe sets or individual probes (it can't reorganize probes into other probe sets). It's also better than simply filtering out the S. pombe probe sets after an ExpressionSet is created, because those unwanted probe sets will still be used in whatever algorithm you used to make the ExpressionSet from the AffyBatch object. All you need is a list of the unwanted probe sets IDs. Let me know if you have any questions. Cheers, Jenny At 01:56 PM 10/1/2008, Hui-Yi Chu wrote: >Hi, > >I am using Affymetrix yeast2 array so that I wanna get rid of S. pombe gene >expression value before further analysis. Earlier I was using filtration >function to filter out the lowest signals which I assumed from S. pombe. >However, this method seems not perfect since I got the result. Thus, I >turned to use altcdfenv package to create a S.C. only env. But I got some >errors when I applied this env for next analysis. I really appreciate your >help!!! > >Here is the code: >## data importing >library("affy") >library("limma") >targets <- readTargets("fed_total.txt") >raw.data <- ReadAffy(filenames = targets $ filename) > >## create altcdfenv >library(altcdfenvs) >getCdfEnvAffy(raw.data); library(yeast2cdf) > >twocdf <- wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf"); print(twocdf) > >sc.ids <- scan("sc_IDs.txt", what="") ### got 5749 s.c. ids >sc.only.cdf <- twocdf[sc.ids] >sc.only.cdf @ envName <- "S_cerevisiae_IDs Only"; print(sc.only.cdf) > >### apply this subset-cdf to "affybatch" >env.sc.cdf <- as(sc.only.cdf, "environment") >raw.data @cdfName <- "sc.only.cdf" >save(raw.data, sc.only.cdf, env.sc.cdf, file="sc_only_cdf.rda") > >### start further analysis >eset <- rma(aaa) > >----- got errors: >Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : > invalid object for 'as.environment' > >### tried pa calls--- also got errors >eset.pm <- mas5calls(raw.data) > >Getting probe level data... >Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : > invalid object for 'as.environment' >Error in as.matrix(pm(object)) : > error in evaluating the argument 'x' in selecting a method for function >'as.matrix' > > >If there is any mistake in my codes???? >Any suggestions are appreciated! > >Many thanks! >Hui-Yi > > > > > sessionInfo() >R version 2.7.2 (2008-08-25) >i386-pc-mingw32 > >locale: >LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >States.1252;LC_MONETARY=English_United >States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > >attached base packages: >[1] splines tools stats graphics grDevices utils datasets >[8] methods base > >other attached packages: > [1] altcdfenvs_2.2.0 hypergraph_1.12.0 Biostrings_2.8.18 > [4] makecdfenv_1.18.0 scatterplot3d_0.3-27 yeast2.db_2.2.0 > [7] affycoretools_1.12.1 annaffy_1.12.1 KEGG.db_2.2.0 >[10] gcrma_2.12.1 matchprobes_1.12.1 biomaRt_1.14.1 >[13] RCurl_0.9-3 GOstats_2.6.0 Category_2.6.0 >[16] RBGL_1.16.0 annotate_1.18.0 xtable_1.5-3 >[19] GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.7-0 >[22] DBI_0.2-4 graph_1.18.1 gplots_2.6.0 >[25] gdata_2.4.2 gtools_2.5.0 Heatplus_1.10.0 >[28] RColorBrewer_1.0-2 genefilter_1.20.0 survival_2.34-1 >[31] yeast2cdf_2.2.0 limma_2.14.6 affy_1.18.2 >[34] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 > >loaded via a namespace (and not attached): >[1] cluster_1.11.11 XML_1.94-0.1 > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu
ADD COMMENTlink written 10.6 years ago by Jenny Drnevich1.9k
Thank you Mark and Jenny!! I agree with Mark, the problem is the "yeast2.db" makes me misunderstand that it is an annotation package with both S. cerevisiae. and S. pombe. This indeed explain my odd result. Not sure if you need it, but here is the S. pombe genome database. HTH. http://www.genedb.org/genedb/pombe/ Thanks Jenny, I will try this long codes and let you know if it works fine for me!!!! Sincerely appreciate your helps. This is a warm maillist. Hui-Yi On Thu, Oct 2, 2008 at 1:10 PM, Jenny Drnevich <drnevich@illinois.edu>wrote: > Hi Hui-Yi, > > See this recent post about another way to remove probe sets: > > https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html > > This will temporarily remove the probe sets from the regular yeast2cdf, and > it's much easier to use than atlcdfenvs if you only want to remove > particular probe sets or individual probes (it can't reorganize probes into > other probe sets). It's also better than simply filtering out the S. pombe > probe sets after an ExpressionSet is created, because those unwanted probe > sets will still be used in whatever algorithm you used to make the > ExpressionSet from the AffyBatch object. All you need is a list of the > unwanted probe sets IDs. Let me know if you have any questions. > > Cheers, > Jenny > > > At 01:56 PM 10/1/2008, Hui-Yi Chu wrote: > >> Hi, >> >> I am using Affymetrix yeast2 array so that I wanna get rid of S. pombe >> gene >> expression value before further analysis. Earlier I was using filtration >> function to filter out the lowest signals which I assumed from S. pombe. >> However, this method seems not perfect since I got the result. Thus, I >> turned to use altcdfenv package to create a S.C. only env. But I got some >> errors when I applied this env for next analysis. I really appreciate your >> help!!! >> >> Here is the code: >> ## data importing >> library("affy") >> library("limma") >> targets <- readTargets("fed_total.txt") >> raw.data <- ReadAffy(filenames = targets $ filename) >> >> ## create altcdfenv >> library(altcdfenvs) >> getCdfEnvAffy(raw.data); library(yeast2cdf) >> >> twocdf <- wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf"); print(twocdf) >> >> sc.ids <- scan("sc_IDs.txt", what="") ### got 5749 s.c. ids >> sc.only.cdf <- twocdf[sc.ids] >> sc.only.cdf @ envName <- "S_cerevisiae_IDs Only"; print(sc.only.cdf) >> >> ### apply this subset-cdf to "affybatch" >> env.sc.cdf <- as(sc.only.cdf, "environment") >> raw.data @cdfName <- "sc.only.cdf" >> save(raw.data, sc.only.cdf, env.sc.cdf, file="sc_only_cdf.rda") >> >> ### start further analysis >> eset <- rma(aaa) >> >> ----- got errors: >> Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : >> invalid object for 'as.environment' >> >> ### tried pa calls--- also got errors >> eset.pm <- mas5calls(raw.data) >> >> Getting probe level data... >> Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : >> invalid object for 'as.environment' >> Error in as.matrix(pm(object)) : >> error in evaluating the argument 'x' in selecting a method for function >> 'as.matrix' >> >> >> If there is any mistake in my codes???? >> Any suggestions are appreciated! >> >> Many thanks! >> Hui-Yi >> >> >> >> > sessionInfo() >> R version 2.7.2 (2008-08-25) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] splines tools stats graphics grDevices utils datasets >> [8] methods base >> >> other attached packages: >> [1] altcdfenvs_2.2.0 hypergraph_1.12.0 Biostrings_2.8.18 >> [4] makecdfenv_1.18.0 scatterplot3d_0.3-27 yeast2.db_2.2.0 >> [7] affycoretools_1.12.1 annaffy_1.12.1 KEGG.db_2.2.0 >> [10] gcrma_2.12.1 matchprobes_1.12.1 biomaRt_1.14.1 >> [13] RCurl_0.9-3 GOstats_2.6.0 Category_2.6.0 >> [16] RBGL_1.16.0 annotate_1.18.0 xtable_1.5-3 >> [19] GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.7-0 >> [22] DBI_0.2-4 graph_1.18.1 gplots_2.6.0 >> [25] gdata_2.4.2 gtools_2.5.0 Heatplus_1.10.0 >> [28] RColorBrewer_1.0-2 genefilter_1.20.0 survival_2.34-1 >> [31] yeast2cdf_2.2.0 limma_2.14.6 affy_1.18.2 >> [34] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.11 XML_1.94-0.1 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich@illinois.edu > [[alternative HTML version deleted]]
ADD REPLYlink written 10.6 years ago by Hui-Yi Chu160
Hi Jenny, These precious codes are really working fine for me!!!!! Also, I went though all of the analysis I knew of the new ExpressionSet and got no problem and more reasonable results even there are still have some blank gene symbols. One more question is I still have to build my own data frame for annotation inforamtion summerization, in this case, I just follow the online BioC manual, but I got the error messege (see below). Codes: ### add annotation info. library("annotate") library("yeast2.db") annotation(esetsub) <- "yeast2.db" # esetsub is a matrix with 5900 rows after removeProbes and filtration probeIDs <- ls(yeast2GENENAME) # Creates vector of all Affy IDs for this chip. symbols <- as.vector(unlist(mget(probeIDs,yeast2GENENAME))) # Retrieves gene descriptions orf <- as.vector(unlist(mget(probeIDs,yeast2ORF))) # Retrieves ORF # build data frame df <- as.data.frame(exprs(esetsub)) Annot <- data.frame(probeIDs, symbols, orf, df, row.names=NULL) ------------Error in data.frame(probeIDs, symbols, orf, df, row.names = NULL) : arguments imply differing number of rows: 10928, 5900 Should I use the same vector as "maskedprobes" to subset the list?? Thank you in advance!!!!!! Best regards, Hui-Yi On Thu, Oct 2, 2008 at 1:10 PM, Jenny Drnevich <drnevich@illinois.edu>wrote: > Hi Hui-Yi, > > See this recent post about another way to remove probe sets: > > https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html > > This will temporarily remove the probe sets from the regular yeast2cdf, and > it's much easier to use than atlcdfenvs if you only want to remove > particular probe sets or individual probes (it can't reorganize probes into > other probe sets). It's also better than simply filtering out the S. pombe > probe sets after an ExpressionSet is created, because those unwanted probe > sets will still be used in whatever algorithm you used to make the > ExpressionSet from the AffyBatch object. All you need is a list of the > unwanted probe sets IDs. Let me know if you have any questions. > > Cheers, > Jenny > > > At 01:56 PM 10/1/2008, Hui-Yi Chu wrote: > >> Hi, >> >> I am using Affymetrix yeast2 array so that I wanna get rid of S. pombe >> gene >> expression value before further analysis. Earlier I was using filtration >> function to filter out the lowest signals which I assumed from S. pombe. >> However, this method seems not perfect since I got the result. Thus, I >> turned to use altcdfenv package to create a S.C. only env. But I got some >> errors when I applied this env for next analysis. I really appreciate your >> help!!! >> >> Here is the code: >> ## data importing >> library("affy") >> library("limma") >> targets <- readTargets("fed_total.txt") >> raw.data <- ReadAffy(filenames = targets $ filename) >> >> ## create altcdfenv >> library(altcdfenvs) >> getCdfEnvAffy(raw.data); library(yeast2cdf) >> >> twocdf <- wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf"); print(twocdf) >> >> sc.ids <- scan("sc_IDs.txt", what="") ### got 5749 s.c. ids >> sc.only.cdf <- twocdf[sc.ids] >> sc.only.cdf @ envName <- "S_cerevisiae_IDs Only"; print(sc.only.cdf) >> >> ### apply this subset-cdf to "affybatch" >> env.sc.cdf <- as(sc.only.cdf, "environment") >> raw.data @cdfName <- "sc.only.cdf" >> save(raw.data, sc.only.cdf, env.sc.cdf, file="sc_only_cdf.rda") >> >> ### start further analysis >> eset <- rma(aaa) >> >> ----- got errors: >> Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : >> invalid object for 'as.environment' >> >> ### tried pa calls--- also got errors >> eset.pm <- mas5calls(raw.data) >> >> Getting probe level data... >> Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : >> invalid object for 'as.environment' >> Error in as.matrix(pm(object)) : >> error in evaluating the argument 'x' in selecting a method for function >> 'as.matrix' >> >> >> If there is any mistake in my codes???? >> Any suggestions are appreciated! >> >> Many thanks! >> Hui-Yi >> >> >> >> > sessionInfo() >> R version 2.7.2 (2008-08-25) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] splines tools stats graphics grDevices utils datasets >> [8] methods base >> >> other attached packages: >> [1] altcdfenvs_2.2.0 hypergraph_1.12.0 Biostrings_2.8.18 >> [4] makecdfenv_1.18.0 scatterplot3d_0.3-27 yeast2.db_2.2.0 >> [7] affycoretools_1.12.1 annaffy_1.12.1 KEGG.db_2.2.0 >> [10] gcrma_2.12.1 matchprobes_1.12.1 biomaRt_1.14.1 >> [13] RCurl_0.9-3 GOstats_2.6.0 Category_2.6.0 >> [16] RBGL_1.16.0 annotate_1.18.0 xtable_1.5-3 >> [19] GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.7-0 >> [22] DBI_0.2-4 graph_1.18.1 gplots_2.6.0 >> [25] gdata_2.4.2 gtools_2.5.0 Heatplus_1.10.0 >> [28] RColorBrewer_1.0-2 genefilter_1.20.0 survival_2.34-1 >> [31] yeast2cdf_2.2.0 limma_2.14.6 affy_1.18.2 >> [34] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.11 XML_1.94-0.1 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich@illinois.edu > [[alternative HTML version deleted]]
ADD REPLYlink written 10.6 years ago by Hui-Yi Chu160
> Hi Hui-Yi, > > See this recent post about another way to remove probe sets: > > https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html > > This will temporarily remove the probe sets from the regular > yeast2cdf, and it's much easier to use than atlcdfenvs if you only want to remove particular probe sets or individual probes (it can't reorganize probes into other probe sets). For removing particular whole probe sets, I would defend that the ease-of-use of "altcdfenvs" is at least as easy (as shown in the vignette "ngenomeschips"). Removing probes within existing probe sets currently requires few lines of code, but I still have the hope to find the time to write either functions or documentation on how to do so in the future. L. > Cheers, > Jenny > > At 01:56 PM 10/1/2008, Hui-Yi Chu wrote: >>Hi, >>I am using Affymetrix yeast2 array so that I wanna get rid of S. pombe >> gene >>expression value before further analysis. Earlier I was using filtration function to filter out the lowest signals which I assumed from S. pombe. However, this method seems not perfect since I got the result. Thus, I turned to use altcdfenv package to create a S.C. only env. But I got some >>errors when I applied this env for next analysis. I really appreciate >> your >>help!!! >>Here is the code: >>## data importing >>library("affy") >>library("limma") >>targets <- readTargets("fed_total.txt") >>raw.data <- ReadAffy(filenames = targets $ filename) >>## create altcdfenv >>library(altcdfenvs) >>getCdfEnvAffy(raw.data); library(yeast2cdf) >>twocdf <- wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf"); print(twocdf) >>sc.ids <- scan("sc_IDs.txt", what="") ### got 5749 s.c. ids sc.only.cdf <- twocdf[sc.ids] >>sc.only.cdf @ envName <- "S_cerevisiae_IDs Only"; print(sc.only.cdf) ### apply this subset-cdf to "affybatch" >>env.sc.cdf <- as(sc.only.cdf, "environment") >>raw.data @cdfName <- "sc.only.cdf" >>save(raw.data, sc.only.cdf, env.sc.cdf, file="sc_only_cdf.rda") >>### start further analysis >>eset <- rma(aaa) >>----- got errors: >>Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : >> invalid object for 'as.environment' >>### tried pa calls--- also got errors >>eset.pm <- mas5calls(raw.data) >>Getting probe level data... >>Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : >> invalid object for 'as.environment' >>Error in as.matrix(pm(object)) : >> error in evaluating the argument 'x' in selecting a method for >> function >>'as.matrix' >>If there is any mistake in my codes???? >>Any suggestions are appreciated! >>Many thanks! >>Hui-Yi >> > sessionInfo() >>R version 2.7.2 (2008-08-25) >>i386-pc-mingw32 >>locale: >>LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>States.1252;LC_MONETARY=English_United >>States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>attached base packages: >>[1] splines tools stats graphics grDevices utils datasets [8] methods base >>other attached packages: >> [1] altcdfenvs_2.2.0 hypergraph_1.12.0 Biostrings_2.8.18 [4] makecdfenv_1.18.0 scatterplot3d_0.3-27 yeast2.db_2.2.0 >> [7] affycoretools_1.12.1 annaffy_1.12.1 KEGG.db_2.2.0 >>[10] gcrma_2.12.1 matchprobes_1.12.1 biomaRt_1.14.1 >>[13] RCurl_0.9-3 GOstats_2.6.0 Category_2.6.0 >>[16] RBGL_1.16.0 annotate_1.18.0 xtable_1.5-3 >>[19] GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.7-0 >>[22] DBI_0.2-4 graph_1.18.1 gplots_2.6.0 >>[25] gdata_2.4.2 gtools_2.5.0 Heatplus_1.10.0 >>[28] RColorBrewer_1.0-2 genefilter_1.20.0 survival_2.34-1 >>[31] yeast2cdf_2.2.0 limma_2.14.6 affy_1.18.2 >>[34] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 >>loaded via a namespace (and not attached): >>[1] cluster_1.11.11 XML_1.94-0.1 >> [[alternative HTML version deleted]] >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >>Search the archives: >>http://news.gmane.org/gmane.science.biology.informatics.conductor > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at illinois.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 10.5 years ago by lgautier@altern.org950
Answer: questions about altcdfenv
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gravatar for Jenny Drnevich
10.6 years ago by
Jenny Drnevich1.9k
United States
Jenny Drnevich1.9k wrote:
Yes, you need to sub-set your probeIDs. You can simply do this to make sure it has the same probesets as your esetsub: probeIDs <- featureNames(esetsub) and then continue with your code. Although I can't guarantee that there won't be other problems... Jenny At 04:36 PM 10/2/2008, Hui-Yi Chu wrote: >Hi Jenny, > >These precious codes are really working fine for me!!!!! >Also, I went though all of the analysis I knew of the new >ExpressionSet and got no problem and more reasonable results even >there are still have some blank gene symbols. One more question is >I still have to build my own data frame for annotation inforamtion >summerization, in this case, I just follow the online BioC >manual, but I got the error messege (see below). > > >Codes: >### add annotation info. >library("annotate") >library("yeast2.db") >annotation(esetsub) <- "yeast2.db" ># esetsub is a matrix with 5900 rows after removeProbes and filtration > >probeIDs <- ls(yeast2GENENAME) # Creates vector of all Affy IDs >for this chip. >symbols <- as.vector(unlist(mget(probeIDs,yeast2GENENAME))) # >Retrieves gene descriptions >orf <- as.vector(unlist(mget(probeIDs,yeast2ORF))) # Retrieves ORF > ># build data frame >df <- as.data.frame(exprs(esetsub)) >Annot <- data.frame(probeIDs, symbols, orf, df, row.names=NULL) >------------Error in data.frame(probeIDs, symbols, orf, df, >row.names = NULL) : > arguments imply differing number of rows: 10928, 5900 > > >Should I use the same vector as "maskedprobes" to subset the list?? >Thank you in advance!!!!!! > >Best regards, >Hui-Yi > > >On Thu, Oct 2, 2008 at 1:10 PM, Jenny Drnevich ><<mailto:drnevich@illinois.edu>drnevich@illinois.edu> wrote: >Hi Hui-Yi, > >See this recent post about another way to remove probe sets: > ><https: stat.ethz.ch="" pipermail="" bioconductor="" 2008-september="" 024296.ht="" ml="">https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.h tml > >This will temporarily remove the probe sets from the regular >yeast2cdf, and it's much easier to use than atlcdfenvs if you only >want to remove particular probe sets or individual probes (it can't >reorganize probes into other probe sets). It's also better than >simply filtering out the S. pombe probe sets after an ExpressionSet >is created, because those unwanted probe sets will still be used in >whatever algorithm you used to make the ExpressionSet from the >AffyBatch object. All you need is a list of the unwanted probe sets >IDs. Let me know if you have any questions. > >Cheers, >Jenny > > >At 01:56 PM 10/1/2008, Hui-Yi Chu wrote: >Hi, > >I am using Affymetrix yeast2 array so that I wanna get rid of S. pombe gene >expression value before further analysis. Earlier I was using filtration >function to filter out the lowest signals which I assumed from S. pombe. >However, this method seems not perfect since I got the result. Thus, I >turned to use altcdfenv package to create a S.C. only env. But I got some >errors when I applied this env for next analysis. I really appreciate your >help!!! > >Here is the code: >## data importing >library("affy") >library("limma") >targets <- readTargets("fed_total.txt") >raw.data <- ReadAffy(filenames = targets $ filename) > >## create altcdfenv >library(altcdfenvs) >getCdfEnvAffy(raw.data); library(yeast2cdf) > >twocdf <- wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf"); print(twocdf) > >sc.ids <- scan("sc_IDs.txt", what="") ### got 5749 s.c. ids >sc.only.cdf <- twocdf[sc.ids] >sc.only.cdf @ envName <- "S_cerevisiae_IDs Only"; print(sc.only.cdf) > >### apply this subset-cdf to "affybatch" >env.sc.cdf <- as(sc.only.cdf, "environment") >raw.data @cdfName <- "sc.only.cdf" >save(raw.data, sc.only.cdf, env.sc.cdf, file="sc_only_cdf.rda") > >### start further analysis >eset <- rma(aaa) > >----- got errors: >Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : > invalid object for 'as.environment' > >### tried pa calls--- also got errors ><http: eset.pm="">eset.pm <- mas5calls(raw.data) > >Getting probe level data... >Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : > invalid object for 'as.environment' >Error in as.matrix(pm(object)) : > error in evaluating the argument 'x' in selecting a method for function >'as.matrix' > > >If there is any mistake in my codes???? >Any suggestions are appreciated! > >Many thanks! >Hui-Yi > > > > > sessionInfo() >R version 2.7.2 (2008-08-25) >i386-pc-mingw32 > >locale: >LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >States.1252;LC_MONETARY=English_United >States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > >attached base packages: >[1] splines tools stats graphics grDevices utils datasets >[8] methods base > >other attached packages: > [1] altcdfenvs_2.2.0 hypergraph_1.12.0 Biostrings_2.8.18 > [4] makecdfenv_1.18.0 scatterplot3d_0.3-27 yeast2.db_2.2.0 > [7] affycoretools_1.12.1 annaffy_1.12.1 KEGG.db_2.2.0 >[10] gcrma_2.12.1 matchprobes_1.12.1 biomaRt_1.14.1 >[13] RCurl_0.9-3 GOstats_2.6.0 Category_2.6.0 >[16] RBGL_1.16.0 annotate_1.18.0 xtable_1.5-3 >[19] GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.7-0 >[22] DBI_0.2-4 graph_1.18.1 gplots_2.6.0 >[25] gdata_2.4.2 gtools_2.5.0 Heatplus_1.10.0 >[28] RColorBrewer_1.0-2 genefilter_1.20.0 survival_2.34-1 >[31] yeast2cdf_2.2.0 limma_2.14.6 affy_1.18.2 >[34] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 > >loaded via a namespace (and not attached): >[1] cluster_1.11.11 XML_1.94-0.1 > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list ><mailto:bioconductor@stat.math.ethz.ch>Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: ><http: news.gmane.org="" gmane.science.biology.informatics.conductor="">ht tp://news.gmane.org/gmane.science.biology.informatics.conductor > > >Jenny Drnevich, Ph.D. > >Functional Genomics Bioinformatics Specialist >W.M. Keck Center for Comparative and Functional Genomics >Roy J. Carver Biotechnology Center >University of Illinois, Urbana-Champaign > >330 ERML >1201 W. Gregory Dr. >Urbana, IL 61801 >USA > >ph: 217-244-7355 >fax: 217-265-5066 >e-mail: <mailto:drnevich@illinois.edu>drnevich@illinois.edu > Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich@illinois.edu [[alternative HTML version deleted]]
ADD COMMENTlink written 10.6 years ago by Jenny Drnevich1.9k
Got it!!! It works well..Thank yo so much... I am really not good in programing.. Many thanks! Hui-Yi On Thu, Oct 2, 2008 at 5:51 PM, Jenny Drnevich <drnevich@illinois.edu>wrote: > Yes, you need to sub-set your probeIDs. You can simply do this to make > sure it has the same probesets as your esetsub: > > probeIDs <- featureNames(esetsub) > > and then continue with your code. Although I can't guarantee that there > won't be other problems... > > Jenny > > > At 04:36 PM 10/2/2008, Hui-Yi Chu wrote: > > Hi Jenny, > > These precious codes are really working fine for me!!!!! > Also, I went though all of the analysis I knew of the new ExpressionSet and > got no problem and more reasonable results even there are still have some > blank gene symbols. One more question is I still have to build my own data > frame for annotation inforamtion summerization, in this case, I just follow > the online BioC manual, but I got the error messege (see below). > > > Codes: > ### add annotation info. > library("annotate") > library("yeast2.db") > annotation(esetsub) <- "yeast2.db" > # esetsub is a matrix with 5900 rows after removeProbes and filtration > > probeIDs <- ls(yeast2GENENAME) # Creates vector of all Affy IDs for > this chip. > symbols <- as.vector(unlist(mget(probeIDs,yeast2GENENAME))) # Retrieves > gene descriptions > orf <- as.vector(unlist(mget(probeIDs,yeast2ORF))) # Retrieves ORF > > # build data frame > df <- as.data.frame(exprs(esetsub)) > Annot <- data.frame(probeIDs, symbols, orf, df, row.names=NULL) > ------------Error in data.frame(probeIDs, symbols, orf, df, row.names = > NULL) : > arguments imply differing number of rows: 10928, 5900 > > > Should I use the same vector as "maskedprobes" to subset the list?? > Thank you in advance!!!!!! > > Best regards, > Hui-Yi > > > On Thu, Oct 2, 2008 at 1:10 PM, Jenny Drnevich <drnevich@illinois.edu> > wrote: > Hi Hui-Yi, > > See this recent post about another way to remove probe sets: > > https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html > > This will temporarily remove the probe sets from the regular yeast2cdf, and > it's much easier to use than atlcdfenvs if you only want to remove > particular probe sets or individual probes (it can't reorganize probes into > other probe sets). It's also better than simply filtering out the S. pombe > probe sets after an ExpressionSet is created, because those unwanted probe > sets will still be used in whatever algorithm you used to make the > ExpressionSet from the AffyBatch object. All you need is a list of the > unwanted probe sets IDs. Let me know if you have any questions. > > Cheers, > Jenny > > > At 01:56 PM 10/1/2008, Hui-Yi Chu wrote: > Hi, > > I am using Affymetrix yeast2 array so that I wanna get rid of S. pombe gene > expression value before further analysis. Earlier I was using filtration > function to filter out the lowest signals which I assumed from S. pombe. > However, this method seems not perfect since I got the result. Thus, I > turned to use altcdfenv package to create a S.C. only env. But I got some > errors when I applied this env for next analysis. I really appreciate your > help!!! > > Here is the code: > ## data importing > library("affy") > library("limma") > targets <- readTargets("fed_total.txt") > raw.data <- ReadAffy(filenames = targets $ filename) > > ## create altcdfenv > library(altcdfenvs) > getCdfEnvAffy(raw.data); library(yeast2cdf) > > twocdf <- wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf"); print(twocdf) > > sc.ids <- scan("sc_IDs.txt", what="") ### got 5749 s.c. ids > sc.only.cdf <- twocdf[sc.ids] > sc.only.cdf @ envName <- "S_cerevisiae_IDs Only"; print(sc.only.cdf) > > ### apply this subset-cdf to "affybatch" > env.sc.cdf <- as(sc.only.cdf, "environment") > raw.data @cdfName <- "sc.only.cdf" > save(raw.data, sc.only.cdf, env.sc.cdf, file="sc_only_cdf.rda") > > ### start further analysis > eset <- rma(aaa) > > ----- got errors: > Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : > invalid object for 'as.environment' > > ### tried pa calls--- also got errors > eset.pm <- mas5calls(raw.data) > > Getting probe level data... > Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : > invalid object for 'as.environment' > Error in as.matrix(pm(object)) : > error in evaluating the argument 'x' in selecting a method for function > 'as.matrix' > > > If there is any mistake in my codes???? > Any suggestions are appreciated! > > Many thanks! > Hui-Yi > > > > > sessionInfo() > R version 2.7.2 (2008-08-25) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] altcdfenvs_2.2.0 hypergraph_1.12.0 Biostrings_2.8.18 > [4] makecdfenv_1.18.0 scatterplot3d_0.3-27 yeast2.db_2.2.0 > [7] affycoretools_1.12.1 annaffy_1.12.1 KEGG.db_2.2.0 > [10] gcrma_2.12.1 matchprobes_1.12.1 biomaRt_1.14.1 > [13] RCurl_0.9-3 GOstats_2.6.0 Category_2.6.0 > [16] RBGL_1.16.0 annotate_1.18.0 xtable_1.5-3 > [19] GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.7-0 > [22] DBI_0.2-4 graph_1.18.1 gplots_2.6.0 > [25] gdata_2.4.2 gtools_2.5.0 Heatplus_1.10.0 > [28] RColorBrewer_1.0-2 genefilter_1.20.0 survival_2.34-1 > [31] yeast2cdf_2.2.0 limma_2.14.6 affy_1.18.2 > [34] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 > > loaded via a namespace (and not attached): > [1] cluster_1.11.11 XML_1.94-0.1 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich@illinois.edu > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich@illinois.edu > [[alternative HTML version deleted]]
ADD REPLYlink written 10.6 years ago by Hui-Yi Chu160
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