Hello group, I know this issue has risen before, but it appears that there was not a final answer to the problem (at least of the latest incident dating June 2007). Similar to others, I am having a difficult time with GDS2eSet. After downloading GDS961 using >gds961<-getGEO("GDS961") I then tried to convert to exprSet using GDS2eSet, and get the following output: > eset961<-GDS2eSet(gds961) trying URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&ac c=GPL91&form=text&view=full' Content type 'geo/text' length unknown opened URL downloaded 13370Kb File stored at: ... Error in validObject(.Object) : invalid class "ExpressionSet" object: featureNames differ between assayData and featureData Here is my session info: > sessionInfo() R version 2.5.1 (2007-06-27) 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] "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: affy affyio GEOquery Biobase limma "1.14.2" "1.4.1" "2.0.5" "1.14.1" "2.10.5" Thanks in advance, Wyatt

Wyatt -- Not that I have a solution, but if I > debug(GDS2eSet) > GDS2eSet(gds961) and then step through the function (pressing the 'n' key) until just before the line "new('ExpressionSet', ...)", and then take a look at the row names of the expression data and of the feature data, I find Browse[1]> which(rownames(expr) != rownames(pData(featuredata))) [1] 12626 12627 12628 12629 12630 12631 12632 12633 12634 12635 12636 12637 [13] 12638 12639 12640 12641 12642 12643 12644 12645 12646 12647 12648 Browse[1]> rownames(expr)[bad] [1] "788_s_at" "119_at" "1215_at" "1216_at" "124_i_at" "125_r_at" [7] "127_at" "1301_s_at" "1302_s_at" "132_at" "1429_at" "1502_s_at" [13] "1829_at" "1864_at" "1889_s_at" "1982_s_at" "36969_at" "383_at" [19] "397_at" "412_s_at" "426_at" "439_at" "787_at" Browse[1]> rownames(pData(featuredata))[bad] [1] "119_at" "1215_at" "1216_at" "124_i_at" "125_r_at" "127_at" [7] "1301_s_at" "1302_s_at" "132_at" "1429_at" "1502_s_at" "1829_at" [13] "1864_at" "1889_s_at" "1982_s_at" "36969_at" "383_at" "397_at" [19] "412_s_at" "426_at" "439_at" "787_at" "788_s_at" Position 12626 seems to be excised and re-inserted at 12648. So the problem is somewhere before the creation of ExpressionSet -- it could be that GDS2eSet needs to sort the rows of featureData to match the order of exprs, or that there is actually an error in the data coming from GEO. The package maintainer (copied on this email; use packageDescription to get this information) will likely chime in. This is in R-2.5.0, like you, or in R-devel, as follows > sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-08 r42441) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY =en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELE PHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GEOquery_2.1.7 RCurl_0.8-1 R.utils_0.9.5 R.oo_1.2.7 [5] Biobase_1.15.23 Martin "Mcmahon, Wyatt" <wyatt.mcmahon at="" ttu.edu=""> writes: > Hello group, > > I know this issue has risen before, but it appears that there was not a final answer to the problem (at least of the latest incident dating June 2007). > > Similar to others, I am having a difficult time with GDS2eSet. After downloading GDS961 using > >>gds961<-getGEO("GDS961") > > I then tried to convert to exprSet using GDS2eSet, and get the following output: > >> eset961<-GDS2eSet(gds961) > trying URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self& acc=GPL91&form=text&view=full' > Content type 'geo/text' length unknown > opened URL > downloaded 13370Kb > File stored at: > ... > Error in validObject(.Object) : invalid class "ExpressionSet" object: featureNames differ between assayData and featureData > > Here is my session info: >> sessionInfo() > R version 2.5.1 (2007-06-27) > 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] "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" > other attached packages: > affy affyio GEOquery Biobase limma > "1.14.2" "1.4.1" "2.0.5" "1.14.1" "2.10.5" > > Thanks in advance, > > Wyatt > > _______________________________________________ > 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 -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org

Thanks so much, Martin! I'm really impressed by the debugging! This is a huge help. I'm sure that Sean will get us the fix very shortly! Thanks guys, Wyatt ________________________________ From: Martin Morgan [mailto:mtmorgan@fhcrc.org] Sent: Wed 8/8/2007 6:53 PM To: Mcmahon, Wyatt Cc: bioconductor at stat.math.ethz.ch; sdavis2 at mail.nih.gov Subject: Re: [BioC] GDS2eSet problems Wyatt -- Not that I have a solution, but if I > debug(GDS2eSet) > GDS2eSet(gds961) and then step through the function (pressing the 'n' key) until just before the line "new('ExpressionSet', ...)", and then take a look at the row names of the expression data and of the feature data, I find Browse[1]> which(rownames(expr) != rownames(pData(featuredata))) [1] 12626 12627 12628 12629 12630 12631 12632 12633 12634 12635 12636 12637 [13] 12638 12639 12640 12641 12642 12643 12644 12645 12646 12647 12648 Browse[1]> rownames(expr)[bad] [1] "788_s_at" "119_at" "1215_at" "1216_at" "124_i_at" "125_r_at" [7] "127_at" "1301_s_at" "1302_s_at" "132_at" "1429_at" "1502_s_at" [13] "1829_at" "1864_at" "1889_s_at" "1982_s_at" "36969_at" "383_at" [19] "397_at" "412_s_at" "426_at" "439_at" "787_at" Browse[1]> rownames(pData(featuredata))[bad] [1] "119_at" "1215_at" "1216_at" "124_i_at" "125_r_at" "127_at" [7] "1301_s_at" "1302_s_at" "132_at" "1429_at" "1502_s_at" "1829_at" [13] "1864_at" "1889_s_at" "1982_s_at" "36969_at" "383_at" "397_at" [19] "412_s_at" "426_at" "439_at" "787_at" "788_s_at" Position 12626 seems to be excised and re-inserted at 12648. So the problem is somewhere before the creation of ExpressionSet -- it could be that GDS2eSet needs to sort the rows of featureData to match the order of exprs, or that there is actually an error in the data coming from GEO. The package maintainer (copied on this email; use packageDescription to get this information) will likely chime in. This is in R-2.5.0, like you, or in R-devel, as follows > sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-08 r42441) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY =en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELE PHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GEOquery_2.1.7 RCurl_0.8-1 R.utils_0.9.5 R.oo_1.2.7 [5] Biobase_1.15.23 Martin "Mcmahon, Wyatt" <wyatt.mcmahon at="" ttu.edu=""> writes: > Hello group, > > I know this issue has risen before, but it appears that there was not a final answer to the problem (at least of the latest incident dating June 2007). > > Similar to others, I am having a difficult time with GDS2eSet. After downloading GDS961 using > >>gds961<-getGEO("GDS961") > > I then tried to convert to exprSet using GDS2eSet, and get the following output: > >> eset961<-GDS2eSet(gds961) > trying URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self& acc=GPL91&form=text&view=full' > Content type 'geo/text' length unknown > opened URL > downloaded 13370Kb > File stored at: > ... > Error in validObject(.Object) : invalid class "ExpressionSet" object: featureNames differ between assayData and featureData > > Here is my session info: >> sessionInfo() > R version 2.5.1 (2007-06-27) > 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] "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" > other attached packages: > affy affyio GEOquery Biobase limma > "1.14.2" "1.4.1" "2.0.5" "1.14.1" "2.10.5" > > Thanks in advance, > > Wyatt > > _______________________________________________ > 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 -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org <http: bioconductor.org=""/>