I am 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?
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2$\begingroup$ Welcome to Bioinformatics.StackExchange @Min! Could you let us know where the instructions indicate that you need the Sp20b_M_v04.cdf file? Is this from a colleague's lab notebook, or from the affy package's documentation, or somewhere else? This info will be helpful in troublehshooting. $\endgroup$– Daniel StandageCommented Mar 4, 2019 at 14:33
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$\begingroup$ Hi Min, completely agree with @DanielStandage. You need to edit your question and add lot more details, otherwise, it's really hard to help. $\endgroup$– Kamil S JaronCommented Mar 4, 2019 at 15:23
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$\begingroup$ @KamilSJaron I converted your answer to a comment since it wasn't really providing a full answer to the question. $\endgroup$– terdon ♦Commented Mar 4, 2019 at 15:27
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$\begingroup$ @terdon I was about to delete it because it was the CEL file I linked, not cdf. ^^ $\endgroup$– Kamil S JaronCommented Mar 4, 2019 at 15:30
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1$\begingroup$ @min I found the corresponding ncbi geo page. it seems that the file you are referring to isn't uploaded. You must contact authors I believe. $\endgroup$– Kamil S JaronCommented Mar 4, 2019 at 15:32
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It looks like it's in GEO here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL10187
There is apparently a zipped copy linked at the bottom in the supplementary files.
When people upload a study based on an array, there is a corresponding 'platform' record where the array details should be deposited.
Edit: you will probably need to gunzip the file first, to get it into CDF format.
