[Bioc-devel] Dimension (rows & columns) in the writeCDF function seems to be swapped

[Groot, Philip de]

Dear Kasper,

I am contacting you because I am puzzled with an issue that is related to affxparser. I submitted this message to the bioc-devel list on april 29 (subject: "RE: [Bioc-devel] FW: problem in ReadAffy function (affy and affyio libraries)") but never received any reply. Interestingly, in the file writeCDF.R (affxparser source) the following comment is present:

# 2006-09-11 /HB
# o BUG FIX: nrows & ncols were swapped in the CDF header.
The problem:
I succesfully created a "mogene11stv1cdf" library that can be used with the "affy" library. Benefit of this is that e.g. the affyPLM library can be used for creating informative plots. I applied rma utilizing affy and oligo and found exactly the same normalized intensities (see attached png-image).

So far so good, BUT... in order to get rma working for affy, I needed to switch the number or rows and columns when creating the CDF-file. And this puzzles me a lot! I do not understand where this originates from.

Let me explain. I use the oligo library and the "pd.mogene.1.1.st.v1" annotation file to create the CDF-file. I (together with Guido Hooiveld) adapted the original "PdInfo2Cdf.R" script for this purpose. Information on the original "PdInfo2Cdf.R" script is here: http://www.aroma-project.org/node/40. The adapted file is also in the attachment.

The CDF-file is created as follows:
source("PdInfo2Cdf.R")
PdInfo2Cdf("pd.mogene.1.1.st.v1", <An appropriate .CEL-file>);

library(makecdfenv)
make.cdf.package(file="pdmogene11stv1.cdf", packagename = "mogene11stv1cdf", author="Philip de Groot", maintainer="Philip de Groot <Philip.deGroot at wur.nl>", version="2.1.0", species="Mus_musculus")

Both CDF-files are available in a single zip-file via sendit:
https://sendit.wur.nl/Download.aspx?id=9299e472-1d5a-4f83-af75-c10aa1faf94c

Does somebody has an explanation for this? Is it a bug in writeCDF?

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
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Dreijenweg 2, 6703 HA  Wageningen
Room: 0052a
T: +31-317-485786
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E-mail:   Philip.deGroot at wur.nl<mailto:Philip.deGroot at wur.nl>
Internet: http://www.nutrigenomicsconsortium.nl<http://www.nutrigenomicsconsortium.nl/>
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