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

Wed Apr 28 22:27:31 CEST 2010

Well, I can investigate further, but this is not the first rectangular
chip encountered by the affyio code. For instance the SNP6.0 array is in a
similar format and can be read successfully as can be seen by examining
images of the intensity data and looking for control regions and so forth.

Furthermore, ReadAffy has always returned columns before rows. Why?
Because that is the historic order in the original text CEL file format.

Ben

> Dear Ben,
>
> ReadAffy is reading the data in incorrectly because the wrong chip
> dimensions are reported. Consequently, the dimension of the intensity
> matrix is also wrong.
>
> 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
> Internet: http://www.nutrigenomicsconsortium.nl
>              http://humannutrition.wur.nl/
>              https://madmax.bioinformatics.nl/
> ________________________________________
> From: bmb at bmbolstad.com [bmb at bmbolstad.com]
> Sent: 28 April 2010 18:26
> To: Groot, Philip de
> Cc: bioc-devel at stat.math.ethz.ch
> Subject: Re: [Bioc-devel] FW: problem in ReadAffy function (affy and
> affyio  libraries)
>
> 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/
>>
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>