[Bioc-devel] FW: problem in ReadAffy function (affy and affyio libraries)

[bmb at bmbolstad.com]

Just to be clear are you reporting that ReadAffy is reading in the data
incorrectly or just that row and column information is reported in
incorrect order?

> I guess that this list is a more appropriate place... (see message below)
>
> Regards,
>
> Dr. Philip de Groot Ph.D.
> Bioinformatics Researcher
>
> Wageningen University / TIFN
> Nutrigenomics Consortium
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> PO Box 8129, 6700 EV Wageningen
> Visiting Address: Erfelijkheidsleer: De Valk, Building 304
> Dreijenweg 2, 6703 HA  Wageningen
> Room: 0052a
> T: +31-317-485786
> F: +31-317-483342
> E-mail:   Philip.deGroot at wur.nl<mailto:Philip.deGroot at wur.nl>
> Internet:
> http://www.nutrigenomicsconsortium.nl<http://www.nutrigenomicsconsortium.nl/>
>              http://humannutrition.wur.nl/
>              https://madmax.bioinformatics.nl/
>
> ________________________________
> From: Groot, Philip de
> Sent: 28 April 2010 16:40
> To: bmb at bmbolstad.com; rafa at jhu.edu
> Cc: bioconductor at stat.math.ethz.ch
> Subject: problem in ReadAffy function (affy and affyio libraries)
>
> Hello all,
>
> I am working with the Affymetrix GeneTitan Gene ST plates ("mogene11stv1"
> arrays). Information on these arrays via the Affymetrix website:
> http://www.affymetrix.com/support/technical/byproduct.affx?product=MoGene-1_1-st-v1
>
> When using the "affy" library to load the .CEL-files, I obtain the
> following AffyBatch object:
>> x <- ReadAffy()
>> x
> AffyBatch object
> size of arrays=990x1190 features (20 kb)
> cdf=MoGene-1_1-st-v1 (35556 affyids)
> number of samples=9
> number of genes=35556
> annotation=mogene11stv1
> notes=
> Please notice that the "size of arrays" is wrong: x and y have been
> switched. When I use the "affxparser" library to obtain the "size of
> arrays" things work out fine:
>> library(affxparser)
>> celHead <- readCelHeader(list.celfiles()[1])
>> c(celHead$rows, celHead$cols)
> [1] 1190  990
> Now the "size of arrays" is correct.
>
> I located the problem in the ReadAffy() function in the following line:
> function: read.celfile.header (called from within the ReadAffy function)
>
>     headdetails <- .Call("ReadHeader", filename, PACKAGE = "affyio")
> As you can see, the actual problem is in the affyio library, where the
> .Call() command returns an inappropriate "headdetails" object.
> Consequently, the dimensions of "exprs(AffyBatch)", after loading the
> .CEL-files, is also wrong.
>
> Note that for the Gene ST version 1.0 arrays the above is not a problem
> because the arrays are square. The Gene ST arrays version 1.1 are
> rectangularly defined. The problem is also present in R-2.10.1.
>
> Can this problem be fixed please?
>
>> sessionInfo()
> R version 2.11.0 (2010-04-22)
> 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] affxparser_1.20.0     mogene11stv1cdf_2.1.0 affy_1.26.0
> [4] Biobase_2.8.0
> loaded via a namespace (and not attached):
> [1] affyio_1.16.0         preprocessCore_1.10.0 tools_2.11.0
> Regards,
>
> Dr. Philip de Groot Ph.D.
> Bioinformatics Researcher
>
> Wageningen University / TIFN
> Nutrigenomics Consortium
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> PO Box 8129, 6700 EV Wageningen
> Visiting Address: Erfelijkheidsleer: De Valk, Building 304
> Dreijenweg 2, 6703 HA  Wageningen
> Room: 0052a
> T: +31-317-485786
> F: +31-317-483342
> E-mail:   Philip.deGroot at wur.nl<mailto:Philip.deGroot at wur.nl>
> Internet:
> http://www.nutrigenomicsconsortium.nl<http://www.nutrigenomicsconsortium.nl/>
>              http://humannutrition.wur.nl/
>              https://madmax.bioinformatics.nl/
>
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