[BioC] SimpeAffy: how to get/generate qcdef file?
Renaud Gaujoux
renaud at mancala.cbio.uct.ac.za
Wed Feb 4 15:22:20 CET 2009
Hi list,
how can one generate the qcdef file required by SimpleAffy in the case
of a sugarcane Affymetrix array.
I installed and loaded the sugarcanecdf package. Since it is in the
Bioconductor repository I thought the qcdef file would come together.
Is there a function that generate the qcdef file automatically from the
cdf file? Ohterwise how does one know what to put in the the qcdef file?
Thank you,
Renaud.
> sessionInfo()
R version 2.8.1 (2008-12-22)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en_ZA.UTF-8;LC_NUMERIC=C;LC_TIME=en_ZA.UTF-8;LC_COLLATE=en_ZA.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_ZA.UTF-8;LC_PAPER=en_ZA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_ZA.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] splines stats graphics grDevices datasets utils
tools methods base
other attached packages:
[1] simpleaffy_2.18.0 genefilter_1.22.0 survival_2.34-1
affyPLM_1.18.1 preprocessCore_1.4.0 gcrma_2.14.1
matchprobes_1.14.1
[8] R2HTML_1.59 AffyExpress_1.8.0 limma_2.16.4
affy_1.20.2 sugarcanecdf_2.3.0 Biobase_2.2.1
loaded via a namespace (and not attached):
[1] affyio_1.10.1 annotate_1.20.1 AnnotationDbi_1.4.2
DBI_0.2-4 RSQLite_0.7-1
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