[BioC] Problems with the package GEOsubission

[Alexandre Kuhn]

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
> 
> 
> 
> 
> 
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