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

Vincent Carey stvjc at channing.harvard.edu
Fri Oct 8 20:35:29 CEST 2010

you certainly don't give many details, like session info or exact
download point for your data.

but i poked around a bit.  perhaps you found a folder


note that these are HT HG U133A -- we do have some metadata packages
for HT arrays, including
the cdf file.  thus you can parse, and upon evaluating the result,
affy will go out and get you the CDF

> x = ReadAffy("5500024030700072107989.H10.CEL")
> x
trying URL 'http://bioconductor.org/packages/2.7/data/annotation/src/contrib/hthgu133acdf_2.7.0.tar.gz'
Content type 'application/x-gzip' length 1738822 bytes (1.7 Mb)
opened URL
downloaded 1.7 Mb

Loading required package: utils
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
* installing *source* package 'hthgu133acdf' ...
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (hthgu133acdf)

The downloaded packages are in
Updating HTML index of packages in '.Library'
AffyBatch object
size of arrays=744x744 features (17 kb)
cdf=HT_HG-U133A (22277 affyids)
number of samples=1
number of genes=22277

> sessionInfo()
R version 2.13.0 Under development (unstable) (2010-09-17 r52943)
Platform: x86_64-unknown-linux-gnu (64-bit)

[1] C

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] hthgu133acdf_2.7.0 affy_1.27.2        Biobase_2.9.1

loaded via a namespace (and not attached):
[1] affyio_1.17.4         preprocessCore_1.11.0 tools_2.13.0

your specific problem needs attention, as the error messages don't seem germane
to reading CEL files, and can probably be made more precise.  but you
have to tell
us more about the environment you are getting this error from

On Fri, Oct 8, 2010 at 12:57 PM, Paul Geeleher <paulgeeleher at gmail.com> wrote:
> Hi,
> 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
> Galway
> Ireland
> --
> www.bioinformaticstutorials.com
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