Question: Where can I find .cdf files for Affymetrix ChIP-chip data analysis?
gravatar for mp
11 months ago by
mp0 wrote:

Hi all

I am in the process of analysing microarray ChIP data generated several years ago. I want to use the affy package for R. However, in order to load the CEL files and proceed with the analysis, I need the pombe annotation file which comes under the name of Sp20b_M_v04.cdf. I have looked everywhere for this file but I am unable to locate it. Is anyone in possession of this file or know where I can download it from? Thank you in advance.

ADD COMMENTlink modified 11 months ago by Benn7.9k • written 11 months ago by mp0

What about GEO? Is this file here as attachment what you need?

ADD REPLYlink written 11 months ago by Benn7.9k


Thank you for your response. I am not sure at this point whether that's the right file or if there's something else wrong. I keep getting the same error still. I load affy and then try to normalise the Data. The working directory is set to a folder containing the CEL and CDF file I downloaded from GEO. The error I am getting reads as follows:

eset <- rma(Data)

Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain Sp20b_M_v04 Library - package sp20bmv04cdf not installed Bioconductor - sp20bmv04cdf not available

Any ideas on what the issue is? Thanks

ADD REPLYlink modified 11 months ago • written 11 months ago by mp0

Maybe install the cdf file first? Did you follow this tutorial?

ADD REPLYlink written 11 months ago by Benn7.9k
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