User: David O. Nelson

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13 years, 7 months ago
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15 years, 5 months ago
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Posts by David O. Nelson

<prev • 6 results • page 1 of 1 • next >
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Comment: C: limma reading genpix files
... Hello all, I've just started plowing thru some two-color arrays and ran across the same bug. The problem I found is due to an efficiency hack that doesn't always work: read.maimages assumes that all the genepix files it reads have the same number of header records. That is, rather than taking the ...
written 13.6 years ago by David O. Nelson60
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Comment: C: MGU74A and MGU74Av2
... On Fri, 2003-06-20 at 11:24, Yongde Bao wrote: > David: > > Can you tell us how you dealt with the masked genes in MG 74A with rma? > I didn't. As I understand RMA (please correct me if I'm wrong here), the default approach is to use Ben Bolstad's quantile normalization followed by a ro ...
written 14.4 years ago by David O. Nelson60
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Comment: C: MGU74A and MGU74Av2
... Our experience with MGU74A and Av2 chips: As I recall, the MGU74A and Av2 have a different number of probe sets! Also, while there is substantial overlap in affy IDs: 1. there are probe set names in A that are not in Av2 (expected), and 2. there are probe set names in A2 that are not in A (NOT exp ...
written 14.4 years ago by David O. Nelson60
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Environments in affy data packages?
... Hi all, The annotation data package for Affy chip hgu133a reveals a number (23 to be exact) of environments, all with names like hgu133aXXXXXXX. While XXXXXX usually makes sense (ACCNUM == accession number, etc), is there a key somewhere that describes in more detail what the environments refer to ...
annotation hgu133a affy written 14.6 years ago by David O. Nelson60 • updated 14.6 years ago by John Zhang2.9k
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Comment: C: Missing file in rhdf5
... Hello all, Regarding the compile failure due to missing rhdf5 files... Might I recommend that rhdf5 not be a part of "...all Bioconductor recommneded (sic) packages in one bundle" ? That way potential users won't be turned off by downloading the package bundle, trying to install it, and being thr ...
written 15.4 years ago by David O. Nelson60
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Answer: A: affy - read.celfile
... In the past (six months ago?), I noticed this type of problem too. What I found was that the read routines had gotten confused by differences in the encoding for newlines on PCs and Unix. In my case, the .cdf files were first transferred to a PC and then copied over to a Unix system. I first encount ...
written 15.4 years ago by David O. Nelson60

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