[BioC] ReadAffy() can't read CEL files from TCGA...

Paul Geeleher paulgeeleher at gmail.com
Fri Oct 8 18:57:13 CEST 2010


I downloaded some glioblastoma hg-u133a CEL files from The Cancer
Genome Atlas (http://cancergenome.nih.gov/) and ReadAffy() can't seem
to load the files. The CEL files are only 5.3 megs each so maybe they
are compressed or something? And when you open them they look like
binary files?

I'm wondering if anybody knows what kind of files these are and how I
might read them? ReadAffy() gives the following error:

> a <- ReadAffy()
Error in value[[3L]](cond) :
  row.names should specify one of the variables
  AnnotatedDataFrame 'initialize' could not update varMetadata:
  perhaps pData and varMetadata are inconsistent?

Paul Geeleher
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland

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