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

[Groot, Philip de]

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/