[BioC] miRNA Array from Affymetrix

Alex Gutteridge alexg at ruggedtextile.com
Mon Dec 6 17:06:22 CET 2010

Just to add on what Guido wrote, I had the same problem with some CEL
files I recently came across and manually setting the CDF to mirna10
to work fine. I've not found any issues with annotation, so I'm assuming
that while kludgy this is OK:

    data = ReadAffy(celfile.path="../data/miRNA_raw_data/") data 

AffyBatch object
size of arrays=230x230 features (40 kb)
cdf=miRNA-1_0_2Xgain (??? affyids)
number of samples=78
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain miRNA-1_0_2Xgain
Library - package mirna102xgaincdf not installed
Bioconductor - mirna102xgaincdf not available
In addition: Warning message:
missing cdf environment! in show(AffyBatch) 

    data = 



AffyBatch object
size of arrays=230x230 features (40 kb)
cdf=mirna10 (7815 affyids)
number of samples=78
number of genes=7815

Alex Gutteridge

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