Question: Problems with the package GEOsubission
0
gravatar for Alexandre Kuhn
8.7 years ago by
Alexandre Kuhn20 wrote:
Hi Fabian, My apologies for taking so long to respond. In your test, you might not have made the right comparison > sampDat <- read.delim(file.path(dataDir, "dRED.txt")) > expMatrix <- read.delim(file.path(dataDir, "eRED.txt")) > colnames(expDat) == sampDat$Sample_supplementary_file I guess that "colnames(expDat)" should be "colnames(expMatrix)". Are you still having this problem you described? Cheers, Alex > Date: Thu, 11 Nov 2010 23:38:24 +0100 > From: Fabian Grammes <fabian.grammes at="" nofima.no=""> > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Problems with the package GEOsubission > Message-ID: > <ofc5426af5.abbab989-onc12577d8.007c0c24-> C12577D8.007C5FFA at nofima.no> > Content-Type: text/plain > > Dear all > > I'm having problems converting my Microarray data (Agilent.txt files) > to > soft files for subission to GEO using the packeage: GEOsubmission > > I have 24 arrays (Agilent.txt files) in my experiment, the files > "eRED.txt" and "dRED.txt" were setup according to the examples given in > the vignette: > > > sampleID <- as.character(c(1:24)) > > seriesName <- "blabla" > > > dataDir <- c("/ArrayDir") > > > microarray2soft(samplenames = sampleID, > + sampleinfo = "dRED.txt", > + seriesnames= seriesName, > + seriesinfo = "ser.txt", > + datadir = dataDir, > + expressionmatrix = "eRED.txt") > > This alway returns the following ERROR messege: > > Error in microarray2soft(samplenames = sampleID, sampleinfo = > "dRED.txt", > : > Column names in expression matrix do not match the names of raw > microarray data files given in sampleinfo file. > > Which is puzzling, because when I read in the .txt files to R and check > the column names for the expressionmatrix and the sample names in the > sampleinfo file I do not find any problems: > > > sampDat <- read.delim(file.path(dataDir, "dRED.txt")) > > expMatrix <- read.delim(file.path(dataDir, "eRED.txt")) > > > colnames(expDat) == sampDat$Sample_supplementary_file > [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > TRUE > TRUE > [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets grid methods > [8] base > > other attached packages: > [1] GEOsubmission_1.2.0 Biobase_2.10.0 limma_3.6.6 > [4] reshape_0.8.3 plyr_1.2.1 proto_0.3-8 > > loaded via a namespace (and not attached): > [1] affy_1.28.0 affyio_1.18.0 ggplot2_0.8.8 > [4] preprocessCore_1.12.0 tools_2.12.0 > > If anyone happens to have any idea what could cause the error message > please let me know > > best regards, Fabian > > > > > > [[alternative HTML version deleted]]
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ADD COMMENTlink modified 8.7 years ago by Fabian Grammes30 • written 8.7 years ago by Alexandre Kuhn20
Answer: Problems with the package GEOsubission
0
gravatar for Fabian Grammes
8.7 years ago by
Fabian Grammes30 wrote:
Thanks for the reply Alex The problem that I had was caused by quotation marks in the colnames from the expression matrix. After removing the quotation marks the function microarray2soft worked well. regrads, Fabian From: "Alexandre Kuhn" <alexandre.m.kuhn@gmail.com> To: "'Fabian Grammes'" <fabian.grammes@nofima.no> Cc: <bioconductor@stat.math.ethz.ch> Date: 12/13/2010 11:18 AM Subject: RE: [BioC] Problems with the package GEOsubission Hi Fabian, My apologies for taking so long to respond. In your test, you might not have made the right comparison > sampDat <- read.delim(file.path(dataDir, "dRED.txt")) > expMatrix <- read.delim(file.path(dataDir, "eRED.txt")) > colnames(expDat) == sampDat$Sample_supplementary_file I guess that "colnames(expDat)" should be "colnames(expMatrix)". Are you still having this problem you described? Cheers, Alex > Date: Thu, 11 Nov 2010 23:38:24 +0100 > From: Fabian Grammes <fabian.grammes@nofima.no> > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] Problems with the package GEOsubission > Message-ID: > <ofc5426af5.abbab989-onc12577d8.007c0c24-> C12577D8.007C5FFA@nofima.no> > Content-Type: text/plain > > Dear all > > I'm having problems converting my Microarray data (Agilent.txt files) > to > soft files for subission to GEO using the packeage: GEOsubmission > > I have 24 arrays (Agilent.txt files) in my experiment, the files > "eRED.txt" and "dRED.txt" were setup according to the examples given in > the vignette: > > > sampleID <- as.character(c(1:24)) > > seriesName <- "blabla" > > > dataDir <- c("/ArrayDir") > > > microarray2soft(samplenames = sampleID, > + sampleinfo = "dRED.txt", > + seriesnames= seriesName, > + seriesinfo = "ser.txt", > + datadir = dataDir, > + expressionmatrix = "eRED.txt") > > This alway returns the following ERROR messege: > > Error in microarray2soft(samplenames = sampleID, sampleinfo = > "dRED.txt", > : > Column names in expression matrix do not match the names of raw > microarray data files given in sampleinfo file. > > Which is puzzling, because when I read in the .txt files to R and check > the column names for the expressionmatrix and the sample names in the > sampleinfo file I do not find any problems: > > > sampDat <- read.delim(file.path(dataDir, "dRED.txt")) > > expMatrix <- read.delim(file.path(dataDir, "eRED.txt")) > > > colnames(expDat) == sampDat$Sample_supplementary_file > [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > TRUE > TRUE > [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets grid methods > [8] base > > other attached packages: > [1] GEOsubmission_1.2.0 Biobase_2.10.0 limma_3.6.6 > [4] reshape_0.8.3 plyr_1.2.1 proto_0.3-8 > > loaded via a namespace (and not attached): > [1] affy_1.28.0 affyio_1.18.0 ggplot2_0.8.8 > [4] preprocessCore_1.12.0 tools_2.12.0 > > If anyone happens to have any idea what could cause the error message > please let me know > > best regards, Fabian > > > > > > [[alternative HTML version deleted]] [[alternative HTML version deleted]]
ADD COMMENTlink written 8.7 years ago by Fabian Grammes30
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