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Dave Jacoby
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20
@dave-jacoby-2272
Last seen 10.1 years ago
I've been trying to get a number of chips to work with the Affy
modules.
I found the
fix for simpleaffy, adding lines to the *.tab files in simplaffy/data,
in the list archives.
(https://stat.ethz.ch/pipermail/bioconductor/2007-February/016033.ht
ml)
Using the techniques listed, I got wheatcdf to work and have sent the
added lines to
the maintainer.
I have added the lines for chickencdf, but I receive the "I don't know
about chip type: chickencdf" error. I am at a loss, as I have done
everything for chickencdf that I have for wheatcdf, with different
result.
alpha.tab: "chickencdf" 0.05 0.065
qc.probes.tab: "chickencdf" "AFFX-Gga-actin-3_at" "AFFX-Gga-actin-
M_at"
"AFFX-Gga-actin-5_a_at" "AFFX-Gga-gapdh-3_a_at" "AFFX-Gga-gapdh-
5_a_at"
"AFFX-Gga-gapdh-M_a_at" "NA" "NA" "NA" "NA" "NA" "NA"
spikes.tab: "chickencdf" "AFFX-Gga-r2-Ec-bioB-3_at"
"AFFX-Gga-r2-Ec-bioB-5_at" "AFFX-Gga-r2-Ec-bioC-3_at"
"AFFX-Gga-r2-P1-cre-3_s_at"
attached base packages:
[1] "splines" "tools" "stats" "graphics" "grDevices"
"datasets"
[7] "utils" "methods" "base"
other attached packages:
chickencdf affyPLM affydata RColorBrewer simpleaffy
genefilter
"1.16.0" "1.12.0" "1.11.2" "0.2-3" "2.10.31"
"1.14.1"
survival limma gcrma matchprobes affy
affyio
"2.31" "2.10.5" "2.8.1" "1.8.1" "1.14.2"
"1.4.0"
Biobase
"1.14.0"
Thanks for any guidance you can give.
--
David Jacoby jacoby at purdue.edu
Purdue Genomics Facility
S049, WSLR building
Phone: hah!