[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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