Question: Where can I find .cdf files for Affymetrix ChIP-chip data analysis?
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gravatar for mp
6 weeks ago by
mp0
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 6 weeks ago by Benn6.6k • written 6 weeks ago by mp0

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

ADD REPLYlink written 6 weeks ago by Benn6.6k

Hi

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 6 weeks ago • written 6 weeks ago by mp0

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

ADD REPLYlink written 6 weeks ago by Benn6.6k
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