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Read .cel file with R program


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#1 MariaAM82

MariaAM82

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Posted 18 February 2013 - 04:57 AM

Hi everybody!

I am trying to read several .cel files from Affymetrix Exon Arrays with the R program. I have loaded the affy, affyio, oligo and pd.huex.1.0.st.v2 packages but when I write the command read.affybatch(dir()[1]) it does not work and the following message appears:

AffyBatch object
size of arrays=2560x2560 features (17 kb)
cdf=HuEx-1_0-st-v2 (??? affyids)
number of samples=1
Error in getCdfInfo(object) :
Could not obtain CDF environment, problems encountered:
Specified environment does not contain HuEx-1_0-st-v2
Library - package huex10stv2cdf not installed
Bioconductor - huex10stv2cdf not available
In addition: Warning messages:
1: In read.affybatch(dir()[1]) :
Incompatible phenoData object. Created a new one.
2: missing cdf environment! in show(AffyBatch)

I have looked for the huex10stv2cdf package through the internet but I cannot find it.

Moreover if I write read.celfile(dir()[1]), a huge list appears without any information even when I ask for it.

Could anyone help me, please? Any advice would be really welcome.

Thanks

Maria




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