problem with justRMA in 2.10.0
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Fraser Sim ▴ 270
@fraser-sim-3567
Last seen 10.2 years ago
I'm getting a cryptic error message when trying to run justRMA on a folder of files, with the file names specified in celFiles. I am not setting the phenoData or protocolData at this point and just want the eset populated with the default pData. This code worked fine under 2.9.2. Thanks, Fraser Here's my code: > library(affy) > eset <- justRMA(filenames = celFiles) Error in validObject(.Object) : invalid class "AffyBatch" object: 1: sample numbers differ between phenoData and protocolData invalid class "AffyBatch" object: 2: sampleNames differ between phenoData and protocolData > all(celFiles %in% list.files()) [1] TRUE > sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] affy_1.24.0 Biobase_2.6.0 rcom_2.2-1 rscproxy_1.3-1 loaded via a namespace (and not attached): [1] affyio_1.14.0 preprocessCore_1.8.0 tools_2.10.0
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@james-w-macdonald-5106
Last seen 2 days ago
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Hi Fraser, Thanks for the bug report. Fixed in devel and released versions now, and should propagate for download within a day or so. Best, Jim Fraser Sim wrote: > I'm getting a cryptic error message when trying to run justRMA on a folder > of files, with the file names specified in celFiles. I am not setting the > phenoData or protocolData at this point and just want the eset populated > with the default pData. This code worked fine under 2.9.2. Thanks, Fraser > > Here's my code: > >> library(affy) >> eset <- justRMA(filenames = celFiles) > Error in validObject(.Object) : > invalid class "AffyBatch" object: 1: sample numbers differ between > phenoData and protocolData > invalid class "AffyBatch" object: 2: sampleNames differ between phenoData > and protocolData >> all(celFiles %in% list.files()) > [1] TRUE >> sessionInfo() > R version 2.10.0 (2009-10-26) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] affy_1.24.0 Biobase_2.6.0 rcom_2.2-1 rscproxy_1.3-1 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 preprocessCore_1.8.0 tools_2.10.0 > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
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Fraser Sim ▴ 270
@fraser-sim-3567
Last seen 10.2 years ago
FYI. This problem was fixed in affy_1.24.1 -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Fraser Sim Sent: Wednesday, November 04, 2009 9:40 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] problem with justRMA in 2.10.0 I'm getting a cryptic error message when trying to run justRMA on a folder of files, with the file names specified in celFiles. I am not setting the phenoData or protocolData at this point and just want the eset populated with the default pData. This code worked fine under 2.9.2. Thanks, Fraser Here's my code: > library(affy) > eset <- justRMA(filenames = celFiles) Error in validObject(.Object) : invalid class "AffyBatch" object: 1: sample numbers differ between phenoData and protocolData invalid class "AffyBatch" object: 2: sampleNames differ between phenoData and protocolData > all(celFiles %in% list.files()) [1] TRUE > sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] affy_1.24.0 Biobase_2.6.0 rcom_2.2-1 rscproxy_1.3-1 loaded via a namespace (and not attached): [1] affyio_1.14.0 preprocessCore_1.8.0 tools_2.10.0 _______________________________________________ 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
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@joseph-dougherty-3787
Last seen 10.2 years ago
Hello, Has this bug been resolved? I am working in R 2.10 for the first time (also a on a new linux server) and I am getting a strange error with ReadAffy(). I don't have this error on my Windows machine, or our old server, which are still on earlier versions of R. > dat<-ReadAffy() Error in value[[3L]](cond) : row names supplied are of the wrong length AnnotatedDataFrame 'initialize' could not update varMetadata: perhaps pData and varMetadata are inconsistent? I am just trying to load all of the Cel files in a directory. I get the same message without a phenoData file (the way I usually run it), or if I make a simple one, which suggests to me this error message is probably not germane. This could also be some other problem with the new server or the R install, but since Frasier had a similar error message, I thought I would check with you all first, before trying to make guess on what else could be going on. I first got the error on Thursday. I deleted and re-installed by bioconductor libraries tonight and stil get the error. Thanks, Joe Dougherty [[alternative HTML version deleted]]
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Hi Joseph, Joseph Dougherty wrote: > Hello, > > Has this bug been resolved? I am working in R 2.10 for the first time (also > a on a new linux server) and I am getting a strange error with ReadAffy(). > I don't have this error on my Windows machine, or our old server, which are > still on earlier versions of R. The bug in justRMA() didn't affect ReadAffy(). >> dat<-ReadAffy() > Error in value[[3L]](cond) : > row names supplied are of the wrong length > AnnotatedDataFrame 'initialize' could not update varMetadata: > perhaps pData and varMetadata are inconsistent? > > I am just trying to load all of the Cel files in a directory. I get the > same message without a phenoData file (the way I usually run it), or if I > make a simple one, which suggests to me this error message is probably not > germane. This could also be some other problem with the new server or > the R install, but since Frasier had a similar error message, I thought I > would check with you all first, before trying to make guess on what else > could be going on. I first got the error on Thursday. I deleted and > re-installed by bioconductor libraries tonight and stil get the error. You always need to supply us with your sessionInfo(). I get this to work with a new version of R, so it is likely you have mis-matched packages. > dat <- ReadAffy() > sessionInfo() R version 2.10.0 Patched (2009-11-05 r50317) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] affy_1.24.1 Biobase_2.6.0 loaded via a namespace (and not attached): [1] affyio_1.14.0 preprocessCore_1.8.0 tools_2.10.0 Best, Jim > > Thanks, > > Joe Dougherty > > [[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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
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> sessionInfo() R version 2.10.0 (2009-10-26) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] gcrma_2.18.0 affy_1.24.1 Biobase_2.6.0 loaded via a namespace (and not attached): [1] affyio_1.14.0 Biostrings_2.14.2 IRanges_1.4.4 [4] preprocessCore_1.8.0 splines_2.10.0 tools_2 The only difference I see is we don't have the patched R 2.10.0. Is that the dev version? Thanks, Joe On Mon, Nov 9, 2009 at 9:25 AM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > Hi Joseph, > > > Joseph Dougherty wrote: > >> Hello, >> >> Has this bug been resolved? I am working in R 2.10 for the first time >> (also >> a on a new linux server) and I am getting a strange error with ReadAffy(). >> I don't have this error on my Windows machine, or our old server, which >> are >> still on earlier versions of R. >> > > The bug in justRMA() didn't affect ReadAffy(). > > > dat<-ReadAffy() >>> >> Error in value[[3L]](cond) : >> row names supplied are of the wrong length >> AnnotatedDataFrame 'initialize' could not update varMetadata: >> perhaps pData and varMetadata are inconsistent? >> >> I am just trying to load all of the Cel files in a directory. I get the >> same message without a phenoData file (the way I usually run it), or if I >> make a simple one, which suggests to me this error message is probably not >> germane. This could also be some other problem with the new server or >> the R install, but since Frasier had a similar error message, I thought I >> would check with you all first, before trying to make guess on what else >> could be going on. I first got the error on Thursday. I deleted and >> re-installed by bioconductor libraries tonight and stil get the error. >> > > You always need to supply us with your sessionInfo(). I get this to work > with a new version of R, so it is likely you have mis-matched packages. > > > dat <- ReadAffy() > > sessionInfo() > R version 2.10.0 Patched (2009-11-05 r50317) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] affy_1.24.1 Biobase_2.6.0 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 preprocessCore_1.8.0 tools_2.10.0 > > Best, > > Jim > > > >> Thanks, >> >> Joe Dougherty >> >> [[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 >> > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > [[alternative HTML version deleted]]
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Joseph Dougherty wrote: > > sessionInfo() > R version 2.10.0 (2009-10-26) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] gcrma_2.18.0 affy_1.24.1 Biobase_2.6.0 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 Biostrings_2.14.2 IRanges_1.4.4 > [4] preprocessCore_1.8.0 splines_2.10.0 tools_2 > > The only difference I see is we don't have the patched R 2.10.0. Is > that the dev version? No, the dev version is R-devel. R-patched is what will be released as R-2.10.1 in a month or so. So it looks like there isn't a mis-matched package here. As of BioC 2.5 we now add scan date information to the AffyBatch, so there are actually two AnnotatedDataFrames being produced. I am betting that the problem is arising when the scan data are put into an AnnotateDataFrame. What do you get if you run the following two functions in the directory that contain your celfiles? fakePheno <- function(){ filenames <- list.celfiles() samplenames <- sub("^/?([^/]*/)*", "", filenames) pdata <- data.frame(sample = seq_len(length(filenames)), row.names = samplenames) phenoData <- new("AnnotatedDataFrame", data = pdata, varMetadata = data.frame(labelDescription = "arbitrary numbering", row.names = "sample")) pData(phenoData) } fakeScan <- function(){ filenames <- list.celfiles() scandates <- sapply(seq_len(length(filenames)), function(x) { sdate <- affyio:::read.celfile.header(filenames[x], info = "full")[["ScanDate"]] if(is.null(sdate)) NA_character_ else sdate }) scandates } Best, Jim > > Thanks, > Joe > > > On Mon, Nov 9, 2009 at 9:25 AM, James W. MacDonald > <jmacdon at="" med.umich.edu="" <mailto:jmacdon="" at="" med.umich.edu="">> wrote: > > Hi Joseph, > > > Joseph Dougherty wrote: > > Hello, > > Has this bug been resolved? I am working in R 2.10 for the > first time (also > a on a new linux server) and I am getting a strange error with > ReadAffy(). > I don't have this error on my Windows machine, or our old > server, which are > still on earlier versions of R. > > > The bug in justRMA() didn't affect ReadAffy(). > > > dat<-ReadAffy() > > Error in value[[3L]](cond) : > row names supplied are of the wrong length > AnnotatedDataFrame 'initialize' could not update varMetadata: > perhaps pData and varMetadata are inconsistent? > > I am just trying to load all of the Cel files in a directory. I > get the > same message without a phenoData file (the way I usually run > it), or if I > make a simple one, which suggests to me this error message is > probably not > germane. This could also be some other problem with the new > server or > the R install, but since Frasier had a similar error message, I > thought I > would check with you all first, before trying to make guess on > what else > could be going on. I first got the error on Thursday. I > deleted and > re-installed by bioconductor libraries tonight and stil get the > error. > > > You always need to supply us with your sessionInfo(). I get this to > work with a new version of R, so it is likely you have mis- matched > packages. > > > dat <- ReadAffy() > > sessionInfo() > R version 2.10.0 Patched (2009-11-05 r50317) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] affy_1.24.1 Biobase_2.6.0 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 preprocessCore_1.8.0 tools_2.10.0 > > Best, > > Jim > > > > Thanks, > > Joe Dougherty > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > <mailto: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 > > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
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fakescan seems to have a problem perhaps: > fakePheno() sample Normal_A10.CEL 1 Normal_C06.CEL 2 Normal_C07.CEL 3 Normal_C08.CEL 4 Normal_C09.CEL 5 Normal_C10.CEL 6 Normal_C11.CEL 7 Normal_D01.CEL 8 Normal_D02.CEL 9 Normal_D03.CEL 10 Tumor7011_A05.CEL 11 Tumor7011_C07.CEL 12 Tumor7011_E05.CEL 13 Tumor7011_F05.CEL 14 Tumor7989_A10.CEL 15 Tumor7989_B08.CEL 16 Tumor7989_C09.CEL 17 Tumor7989_C10.CEL 18 Tumor7989_D10.CEL 19 Tumor7989_F08.CEL 20 Tumor7989_F09.CEL 21 Tumor7989_G09.CEL 22 Tumor7989_G10.CEL 23 Tumor7989_H03.CEL 24 Tumor7989_H09.CEL 25 Tumor7996_B03.CEL 26 Tumor7996_B06.CEL 27 Tumor7996_D06.CEL 28 Tumor7996_F06.CEL 29 Tumor8340_A02.CEL 30 Tumor8340_A03.CEL 31 Tumor8340_A04.CEL 32 Tumor8340_A09.CEL 33 Tumor8340_A10.CEL 34 Tumor8340_B07.CEL 35 Tumor8340_B08.CEL 36 Tumor8340_B09.CEL 37 Tumor8340_B11.CEL 38 Tumor8340_B12.CEL 39 Tumor8340_C05.CEL 40 Tumor8340_C06.CEL 41 Tumor8340_C07.CEL 42 Tumor8340_C08.CEL 43 Tumor8340_C09.CEL 44 Tumor8340_D01.CEL 45 Tumor8340_E03.CEL 46 Tumor8340_E08.CEL 47 Tumor8340_F03.CEL 48 Tumor8340_F07.CEL 49 Tumor8461_A02.CEL 50 Tumor8461_C01.CEL 51 Tumor8461_C06.CEL 52 Tumor8461_C12.CEL 53 Tumor8615_A05.CEL 54 Tumor8615_A06.CEL 55 Tumor8615_A07.CEL 56 Tumor8615_A10.CEL 57 Tumor8615_B01.CEL 58 Tumor8615_B08.CEL 59 Tumor8615_B10.CEL 60 Tumor8615_C01.CEL 61 Tumor8615_C02.CEL 62 Tumor8615_C08.CEL 63 Tumor8615_C10.CEL 64 Tumor8615_E07.CEL 65 Tumor8615_F01.CEL 66 Tumor8615_F03.CEL 67 Tumor8615_F07.CEL 68 Tumor8615_H09.CEL 69 > fakeScan() [[1]] character(0) [[2]] character(0) [[3]] character(0) [[4]] character(0) [[5]] character(0) [[6]] character(0) [[7]] character(0) [[8]] character(0) [[9]] character(0) [[10]] character(0) [[11]] character(0) [[12]] character(0) [[13]] character(0) [[14]] character(0) [[15]] character(0) [[16]] character(0) [[17]] character(0) [[18]] character(0) [[19]] character(0) [[20]] character(0) [[21]] character(0) [[22]] character(0) [[23]] character(0) [[24]] character(0) [[25]] character(0) [[26]] character(0) [[27]] character(0) [[28]] character(0) [[29]] character(0) [[30]] character(0) [[31]] character(0) [[32]] character(0) [[33]] character(0) [[34]] character(0) [[35]] character(0) [[36]] character(0) [[37]] character(0) [[38]] character(0) [[39]] character(0) [[40]] character(0) [[41]] character(0) [[42]] character(0) [[43]] character(0) [[44]] character(0) [[45]] character(0) [[46]] character(0) [[47]] character(0) [[48]] character(0) [[49]] character(0) [[50]] character(0) [[51]] character(0) [[52]] character(0) [[53]] character(0) [[54]] character(0) [[55]] character(0) [[56]] character(0) [[57]] character(0) [[58]] character(0) [[59]] character(0) [[60]] character(0) [[61]] character(0) [[62]] character(0) [[63]] character(0) [[64]] character(0) [[65]] character(0) [[66]] character(0) [[67]] character(0) [[68]] character(0) [[69]] character(0) On Mon, Nov 9, 2009 at 2:24 PM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > > > Joseph Dougherty wrote: > >> > sessionInfo() >> R version 2.10.0 (2009-10-26) >> x86_64-unknown-linux-gnu >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] gcrma_2.18.0 affy_1.24.1 Biobase_2.6.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.14.0 Biostrings_2.14.2 IRanges_1.4.4 >> [4] preprocessCore_1.8.0 splines_2.10.0 tools_2 >> >> The only difference I see is we don't have the patched R 2.10.0. Is that >> the dev version? >> > > No, the dev version is R-devel. R-patched is what will be released as > R-2.10.1 in a month or so. > > So it looks like there isn't a mis-matched package here. As of BioC 2.5 we > now add scan date information to the AffyBatch, so there are actually two > AnnotatedDataFrames being produced. I am betting that the problem is arising > when the scan data are put into an AnnotateDataFrame. > > What do you get if you run the following two functions in the directory > that contain your celfiles? > > fakePheno <- function(){ > filenames <- list.celfiles() > samplenames <- sub("^/?([^/]*/)*", "", filenames) > pdata <- data.frame(sample = seq_len(length(filenames)), row.names = > samplenames) > phenoData <- new("AnnotatedDataFrame", data = pdata, > varMetadata = data.frame(labelDescription = "arbitrary > numbering", > row.names = "sample")) > pData(phenoData) > } > > fakeScan <- function(){ > filenames <- list.celfiles() > scandates <- sapply(seq_len(length(filenames)), function(x) { > sdate <- affyio:::read.celfile.header(filenames[x], info = > "full")[["ScanDate"]] > if(is.null(sdate)) > NA_character_ > else > sdate > }) > scandates > } > > Best, > > Jim > > > > >> Thanks, >> Joe >> >> >> >> On Mon, Nov 9, 2009 at 9:25 AM, James W. MacDonald <jmacdon@med.umich.edu<mailto:>> jmacdon@med.umich.edu>> wrote: >> >> Hi Joseph, >> >> >> Joseph Dougherty wrote: >> >> Hello, >> >> Has this bug been resolved? I am working in R 2.10 for the >> first time (also >> a on a new linux server) and I am getting a strange error with >> ReadAffy(). >> I don't have this error on my Windows machine, or our old >> server, which are >> still on earlier versions of R. >> >> >> The bug in justRMA() didn't affect ReadAffy(). >> >> >> dat<-ReadAffy() >> >> Error in value[[3L]](cond) : >> row names supplied are of the wrong length >> AnnotatedDataFrame 'initialize' could not update varMetadata: >> perhaps pData and varMetadata are inconsistent? >> >> I am just trying to load all of the Cel files in a directory. I >> get the >> same message without a phenoData file (the way I usually run >> it), or if I >> make a simple one, which suggests to me this error message is >> probably not >> germane. This could also be some other problem with the new >> server or >> the R install, but since Frasier had a similar error message, I >> thought I >> would check with you all first, before trying to make guess on >> what else >> could be going on. I first got the error on Thursday. I >> deleted and >> re-installed by bioconductor libraries tonight and stil get the >> error. >> >> >> You always need to supply us with your sessionInfo(). I get this to >> work with a new version of R, so it is likely you have mis- matched >> packages. >> >> > dat <- ReadAffy() >> > sessionInfo() >> R version 2.10.0 Patched (2009-11-05 r50317) >> i386-pc-mingw32 >> >> locale: >> [1] LC_COLLATE=English_United States.1252 >> [2] LC_CTYPE=English_United States.1252 >> [3] LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> other attached packages: >> [1] affy_1.24.1 Biobase_2.6.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.14.0 preprocessCore_1.8.0 tools_2.10.0 >> >> Best, >> >> Jim >> >> >> >> Thanks, >> >> Joe Dougherty >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> <mailto:bioconductor@stat.math.ethz.ch> >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> >> >> > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > [[alternative HTML version deleted]]
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What do you get from affyio:::read.celfile.header(list.celfiles()[1], info = "full") Joseph Dougherty wrote: > fakescan seems to have a problem perhaps: > > > fakePheno() > sample > Normal_A10.CEL 1 > Normal_C06.CEL 2 > Normal_C07.CEL 3 > Normal_C08.CEL 4 > Normal_C09.CEL 5 > Normal_C10.CEL 6 > Normal_C11.CEL 7 > Normal_D01.CEL 8 > Normal_D02.CEL 9 > Normal_D03.CEL 10 > Tumor7011_A05.CEL 11 > Tumor7011_C07.CEL 12 > Tumor7011_E05.CEL 13 > Tumor7011_F05.CEL 14 > Tumor7989_A10.CEL 15 > Tumor7989_B08.CEL 16 > Tumor7989_C09.CEL 17 > Tumor7989_C10.CEL 18 > Tumor7989_D10.CEL 19 > Tumor7989_F08.CEL 20 > Tumor7989_F09.CEL 21 > Tumor7989_G09.CEL 22 > Tumor7989_G10.CEL 23 > Tumor7989_H03.CEL 24 > Tumor7989_H09.CEL 25 > Tumor7996_B03.CEL 26 > Tumor7996_B06.CEL 27 > Tumor7996_D06.CEL 28 > Tumor7996_F06.CEL 29 > Tumor8340_A02.CEL 30 > Tumor8340_A03.CEL 31 > Tumor8340_A04.CEL 32 > Tumor8340_A09.CEL 33 > Tumor8340_A10.CEL 34 > Tumor8340_B07.CEL 35 > Tumor8340_B08.CEL 36 > Tumor8340_B09.CEL 37 > Tumor8340_B11.CEL 38 > Tumor8340_B12.CEL 39 > Tumor8340_C05.CEL 40 > Tumor8340_C06.CEL 41 > Tumor8340_C07.CEL 42 > Tumor8340_C08.CEL 43 > Tumor8340_C09.CEL 44 > Tumor8340_D01.CEL 45 > Tumor8340_E03.CEL 46 > Tumor8340_E08.CEL 47 > Tumor8340_F03.CEL 48 > Tumor8340_F07.CEL 49 > Tumor8461_A02.CEL 50 > Tumor8461_C01.CEL 51 > Tumor8461_C06.CEL 52 > Tumor8461_C12.CEL 53 > Tumor8615_A05.CEL 54 > Tumor8615_A06.CEL 55 > Tumor8615_A07.CEL 56 > Tumor8615_A10.CEL 57 > Tumor8615_B01.CEL 58 > Tumor8615_B08.CEL 59 > Tumor8615_B10.CEL 60 > Tumor8615_C01.CEL 61 > Tumor8615_C02.CEL 62 > Tumor8615_C08.CEL 63 > Tumor8615_C10.CEL 64 > Tumor8615_E07.CEL 65 > Tumor8615_F01.CEL 66 > Tumor8615_F03.CEL 67 > Tumor8615_F07.CEL 68 > Tumor8615_H09.CEL 69 > > > fakeScan() > [[1]] > character(0) > > [[2]] > character(0) > > [[3]] > character(0) > > [[4]] > character(0) > > [[5]] > character(0) > > [[6]] > character(0) > > [[7]] > character(0) > > [[8]] > character(0) > > [[9]] > character(0) > > [[10]] > character(0) > > [[11]] > character(0) > > [[12]] > character(0) > > [[13]] > character(0) > > [[14]] > character(0) > > [[15]] > character(0) > > [[16]] > character(0) > > [[17]] > character(0) > > [[18]] > character(0) > > [[19]] > character(0) > > [[20]] > character(0) > > [[21]] > character(0) > > [[22]] > character(0) > > [[23]] > character(0) > > [[24]] > character(0) > > [[25]] > character(0) > > [[26]] > character(0) > > [[27]] > character(0) > > [[28]] > character(0) > > [[29]] > character(0) > > [[30]] > character(0) > > [[31]] > character(0) > > [[32]] > character(0) > > [[33]] > character(0) > > [[34]] > character(0) > > [[35]] > character(0) > > [[36]] > character(0) > > [[37]] > character(0) > > [[38]] > character(0) > > [[39]] > character(0) > > [[40]] > character(0) > > [[41]] > character(0) > > [[42]] > character(0) > > [[43]] > character(0) > > [[44]] > character(0) > > [[45]] > character(0) > > [[46]] > character(0) > > [[47]] > character(0) > > [[48]] > character(0) > > [[49]] > character(0) > > [[50]] > character(0) > > [[51]] > character(0) > > [[52]] > character(0) > > [[53]] > character(0) > > [[54]] > character(0) > > [[55]] > character(0) > > [[56]] > character(0) > > [[57]] > character(0) > > [[58]] > character(0) > > [[59]] > character(0) > > [[60]] > character(0) > > [[61]] > character(0) > > [[62]] > character(0) > > [[63]] > character(0) > > [[64]] > character(0) > > [[65]] > character(0) > > [[66]] > character(0) > > [[67]] > character(0) > > [[68]] > character(0) > > [[69]] > character(0) > > > On Mon, Nov 9, 2009 at 2:24 PM, James W. MacDonald > <jmacdon at="" med.umich.edu="" <mailto:jmacdon="" at="" med.umich.edu="">> wrote: > > > > Joseph Dougherty wrote: > > > sessionInfo() > R version 2.10.0 (2009-10-26) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] gcrma_2.18.0 affy_1.24.1 Biobase_2.6.0 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 Biostrings_2.14.2 IRanges_1.4.4 > [4] preprocessCore_1.8.0 splines_2.10.0 tools_2 > > The only difference I see is we don't have the patched R 2.10.0. > Is that the dev version? > > > No, the dev version is R-devel. R-patched is what will be released > as R-2.10.1 in a month or so. > > So it looks like there isn't a mis-matched package here. As of BioC > 2.5 we now add scan date information to the AffyBatch, so there are > actually two AnnotatedDataFrames being produced. I am betting that > the problem is arising when the scan data are put into an > AnnotateDataFrame. > > What do you get if you run the following two functions in the > directory that contain your celfiles? > > fakePheno <- function(){ > filenames <- list.celfiles() > samplenames <- sub("^/?([^/]*/)*", "", filenames) > pdata <- data.frame(sample = seq_len(length(filenames)), > row.names = samplenames) > phenoData <- new("AnnotatedDataFrame", data = pdata, > varMetadata = data.frame(labelDescription = "arbitrary > numbering", > row.names = "sample")) > pData(phenoData) > } > > fakeScan <- function(){ > filenames <- list.celfiles() > scandates <- sapply(seq_len(length(filenames)), function(x) { > sdate <- affyio:::read.celfile.header(filenames[x], info = > "full")[["ScanDate"]] > if(is.null(sdate)) > NA_character_ > else > sdate > }) > scandates > } > > Best, > > Jim > > > > > Thanks, > Joe > > > > On Mon, Nov 9, 2009 at 9:25 AM, James W. MacDonald > <jmacdon at="" med.umich.edu="" <mailto:jmacdon="" at="" med.umich.edu=""> > <mailto:jmacdon at="" med.umich.edu="" <mailto:jmacdon="" at="" med.umich.edu="">>> > wrote: > > Hi Joseph, > > > Joseph Dougherty wrote: > > Hello, > > Has this bug been resolved? I am working in R 2.10 for the > first time (also > a on a new linux server) and I am getting a strange error > with > ReadAffy(). > I don't have this error on my Windows machine, or our old > server, which are > still on earlier versions of R. > > > The bug in justRMA() didn't affect ReadAffy(). > > > dat<-ReadAffy() > > Error in value[[3L]](cond) : > row names supplied are of the wrong length > AnnotatedDataFrame 'initialize' could not update > varMetadata: > perhaps pData and varMetadata are inconsistent? > > I am just trying to load all of the Cel files in a > directory. I > get the > same message without a phenoData file (the way I usually run > it), or if I > make a simple one, which suggests to me this error message is > probably not > germane. This could also be some other problem with > the new > server or > the R install, but since Frasier had a similar error > message, I > thought I > would check with you all first, before trying to make > guess on > what else > could be going on. I first got the error on Thursday. I > deleted and > re-installed by bioconductor libraries tonight and stil > get the > error. > > > You always need to supply us with your sessionInfo(). I get > this to > work with a new version of R, so it is likely you have > mis-matched > packages. > > > dat <- ReadAffy() > > sessionInfo() > R version 2.10.0 Patched (2009-11-05 r50317) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods > base > > other attached packages: > [1] affy_1.24.1 Biobase_2.6.0 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 preprocessCore_1.8.0 tools_2.10.0 > > Best, > > Jim > > > > Thanks, > > Joe Dougherty > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > <mailto:bioconductor at="" stat.math.ethz.ch=""> > <mailto:bioconductor at="" stat.math.ethz.ch=""> <mailto: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 > > > -- James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
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Entering edit mode
This has been fixed in both the devel (1.25.2) and release (1.24.2) versions of affy. You can either wait for it to propagate through the build system (1-2 days) or get it from svn. Best, Jim Joseph Dougherty wrote: > fakescan seems to have a problem perhaps: > >> fakePheno() > sample > Normal_A10.CEL 1 > Normal_C06.CEL 2 > Normal_C07.CEL 3 > Normal_C08.CEL 4 > Normal_C09.CEL 5 > Normal_C10.CEL 6 > Normal_C11.CEL 7 > Normal_D01.CEL 8 > Normal_D02.CEL 9 > Normal_D03.CEL 10 > Tumor7011_A05.CEL 11 > Tumor7011_C07.CEL 12 > Tumor7011_E05.CEL 13 > Tumor7011_F05.CEL 14 > Tumor7989_A10.CEL 15 > Tumor7989_B08.CEL 16 > Tumor7989_C09.CEL 17 > Tumor7989_C10.CEL 18 > Tumor7989_D10.CEL 19 > Tumor7989_F08.CEL 20 > Tumor7989_F09.CEL 21 > Tumor7989_G09.CEL 22 > Tumor7989_G10.CEL 23 > Tumor7989_H03.CEL 24 > Tumor7989_H09.CEL 25 > Tumor7996_B03.CEL 26 > Tumor7996_B06.CEL 27 > Tumor7996_D06.CEL 28 > Tumor7996_F06.CEL 29 > Tumor8340_A02.CEL 30 > Tumor8340_A03.CEL 31 > Tumor8340_A04.CEL 32 > Tumor8340_A09.CEL 33 > Tumor8340_A10.CEL 34 > Tumor8340_B07.CEL 35 > Tumor8340_B08.CEL 36 > Tumor8340_B09.CEL 37 > Tumor8340_B11.CEL 38 > Tumor8340_B12.CEL 39 > Tumor8340_C05.CEL 40 > Tumor8340_C06.CEL 41 > Tumor8340_C07.CEL 42 > Tumor8340_C08.CEL 43 > Tumor8340_C09.CEL 44 > Tumor8340_D01.CEL 45 > Tumor8340_E03.CEL 46 > Tumor8340_E08.CEL 47 > Tumor8340_F03.CEL 48 > Tumor8340_F07.CEL 49 > Tumor8461_A02.CEL 50 > Tumor8461_C01.CEL 51 > Tumor8461_C06.CEL 52 > Tumor8461_C12.CEL 53 > Tumor8615_A05.CEL 54 > Tumor8615_A06.CEL 55 > Tumor8615_A07.CEL 56 > Tumor8615_A10.CEL 57 > Tumor8615_B01.CEL 58 > Tumor8615_B08.CEL 59 > Tumor8615_B10.CEL 60 > Tumor8615_C01.CEL 61 > Tumor8615_C02.CEL 62 > Tumor8615_C08.CEL 63 > Tumor8615_C10.CEL 64 > Tumor8615_E07.CEL 65 > Tumor8615_F01.CEL 66 > Tumor8615_F03.CEL 67 > Tumor8615_F07.CEL 68 > Tumor8615_H09.CEL 69 > >> fakeScan() > [[1]] > character(0) > > [[2]] > character(0) > > [[3]] > character(0) > > [[4]] > character(0) > > [[5]] > character(0) > > [[6]] > character(0) > > [[7]] > character(0) > > [[8]] > character(0) > > [[9]] > character(0) > > [[10]] > character(0) > > [[11]] > character(0) > > [[12]] > character(0) > > [[13]] > character(0) > > [[14]] > character(0) > > [[15]] > character(0) > > [[16]] > character(0) > > [[17]] > character(0) > > [[18]] > character(0) > > [[19]] > character(0) > > [[20]] > character(0) > > [[21]] > character(0) > > [[22]] > character(0) > > [[23]] > character(0) > > [[24]] > character(0) > > [[25]] > character(0) > > [[26]] > character(0) > > [[27]] > character(0) > > [[28]] > character(0) > > [[29]] > character(0) > > [[30]] > character(0) > > [[31]] > character(0) > > [[32]] > character(0) > > [[33]] > character(0) > > [[34]] > character(0) > > [[35]] > character(0) > > [[36]] > character(0) > > [[37]] > character(0) > > [[38]] > character(0) > > [[39]] > character(0) > > [[40]] > character(0) > > [[41]] > character(0) > > [[42]] > character(0) > > [[43]] > character(0) > > [[44]] > character(0) > > [[45]] > character(0) > > [[46]] > character(0) > > [[47]] > character(0) > > [[48]] > character(0) > > [[49]] > character(0) > > [[50]] > character(0) > > [[51]] > character(0) > > [[52]] > character(0) > > [[53]] > character(0) > > [[54]] > character(0) > > [[55]] > character(0) > > [[56]] > character(0) > > [[57]] > character(0) > > [[58]] > character(0) > > [[59]] > character(0) > > [[60]] > character(0) > > [[61]] > character(0) > > [[62]] > character(0) > > [[63]] > character(0) > > [[64]] > character(0) > > [[65]] > character(0) > > [[66]] > character(0) > > [[67]] > character(0) > > [[68]] > character(0) > > [[69]] > character(0) > > > On Mon, Nov 9, 2009 at 2:24 PM, James W. MacDonald <jmacdon at="" med.umich.edu="">wrote: > >> >> Joseph Dougherty wrote: >> >>> > sessionInfo() >>> R version 2.10.0 (2009-10-26) >>> x86_64-unknown-linux-gnu >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] gcrma_2.18.0 affy_1.24.1 Biobase_2.6.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.14.0 Biostrings_2.14.2 IRanges_1.4.4 >>> [4] preprocessCore_1.8.0 splines_2.10.0 tools_2 >>> >>> The only difference I see is we don't have the patched R 2.10.0. Is that >>> the dev version? >>> >> No, the dev version is R-devel. R-patched is what will be released as >> R-2.10.1 in a month or so. >> >> So it looks like there isn't a mis-matched package here. As of BioC 2.5 we >> now add scan date information to the AffyBatch, so there are actually two >> AnnotatedDataFrames being produced. I am betting that the problem is arising >> when the scan data are put into an AnnotateDataFrame. >> >> What do you get if you run the following two functions in the directory >> that contain your celfiles? >> >> fakePheno <- function(){ >> filenames <- list.celfiles() >> samplenames <- sub("^/?([^/]*/)*", "", filenames) >> pdata <- data.frame(sample = seq_len(length(filenames)), row.names = >> samplenames) >> phenoData <- new("AnnotatedDataFrame", data = pdata, >> varMetadata = data.frame(labelDescription = "arbitrary >> numbering", >> row.names = "sample")) >> pData(phenoData) >> } >> >> fakeScan <- function(){ >> filenames <- list.celfiles() >> scandates <- sapply(seq_len(length(filenames)), function(x) { >> sdate <- affyio:::read.celfile.header(filenames[x], info = >> "full")[["ScanDate"]] >> if(is.null(sdate)) >> NA_character_ >> else >> sdate >> }) >> scandates >> } >> >> Best, >> >> Jim >> >> >> >> >>> Thanks, >>> Joe >>> >>> >>> >>> On Mon, Nov 9, 2009 at 9:25 AM, James W. MacDonald <jmacdon at="" med.umich.edu<mailto:="">>> jmacdon at med.umich.edu>> wrote: >>> >>> Hi Joseph, >>> >>> >>> Joseph Dougherty wrote: >>> >>> Hello, >>> >>> Has this bug been resolved? I am working in R 2.10 for the >>> first time (also >>> a on a new linux server) and I am getting a strange error with >>> ReadAffy(). >>> I don't have this error on my Windows machine, or our old >>> server, which are >>> still on earlier versions of R. >>> >>> >>> The bug in justRMA() didn't affect ReadAffy(). >>> >>> >>> dat<-ReadAffy() >>> >>> Error in value[[3L]](cond) : >>> row names supplied are of the wrong length >>> AnnotatedDataFrame 'initialize' could not update varMetadata: >>> perhaps pData and varMetadata are inconsistent? >>> >>> I am just trying to load all of the Cel files in a directory. I >>> get the >>> same message without a phenoData file (the way I usually run >>> it), or if I >>> make a simple one, which suggests to me this error message is >>> probably not >>> germane. This could also be some other problem with the new >>> server or >>> the R install, but since Frasier had a similar error message, I >>> thought I >>> would check with you all first, before trying to make guess on >>> what else >>> could be going on. I first got the error on Thursday. I >>> deleted and >>> re-installed by bioconductor libraries tonight and stil get the >>> error. >>> >>> >>> You always need to supply us with your sessionInfo(). I get this to >>> work with a new version of R, so it is likely you have mis- matched >>> packages. >>> >>> > dat <- ReadAffy() >>> > sessionInfo() >>> R version 2.10.0 Patched (2009-11-05 r50317) >>> i386-pc-mingw32 >>> >>> locale: >>> [1] LC_COLLATE=English_United States.1252 >>> [2] LC_CTYPE=English_United States.1252 >>> [3] LC_MONETARY=English_United States.1252 >>> [4] LC_NUMERIC=C >>> [5] LC_TIME=English_United States.1252 >>> >>> attached base packages: >>> [1] stats graphics grDevices datasets utils methods base >>> >>> other attached packages: >>> [1] affy_1.24.1 Biobase_2.6.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.14.0 preprocessCore_1.8.0 tools_2.10.0 >>> >>> Best, >>> >>> Jim >>> >>> >>> >>> Thanks, >>> >>> Joe Dougherty >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> <mailto: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 >>> >>> >>> -- James W. MacDonald, M.S. >>> Biostatistician >>> Douglas Lab >>> University of Michigan >>> Department of Human Genetics >>> 5912 Buhl >>> 1241 E. Catherine St. >>> Ann Arbor MI 48109-5618 >>> 734-615-7826 >>> >>> >>> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> > > [[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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
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