Hello,

I am trying to analyze microarray data (E-BUGS-55 and E-BUGS-56) and I am not sure if you could guide me to some code that can be used to analyze this type of affymetrix arrays. I am currently running into trouble as I need to construct cdf files but I am not sure how I can do so.

I would really appreciate ur help!

E-BUGS-55 and E-BUGS-56 are ArrayExpress IDs for two experiments that were analyzed using some spotted cDNA arrays. These are not Affymetrix arrays! In addition, you should hypothetically be able to process the data using the ArrayExpress package. However, I get an error that I don't have time to track down:

> z <- ArrayExpress("E-BUGS-56")
trying URL 'http://www.ebi.ac.uk/arrayexpress/files/A-BUGS-20/A-BUGS-20.adf.txt'
Content type 'text/plain' length 5178761 bytes (4.9 MB)
==================================================
downloaded 4.9 MB

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-BUGS-56/E-BUGS-56.sdrf.txt'
Content type 'text/plain' length 36395 bytes (35 KB)
==================================================
downloaded 35 KB

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-BUGS-56/E-BUGS-56.idf.txt'
Content type 'text/plain' length 13006 bytes (12 KB)
==================================================
downloaded 12 KB

Copying raw data files

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-BUGS-56/E-BUGS-56.raw.1.zip'
Content type 'application/zip' length 1535370 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

Unpacking data files
ArrayExpress: Reading pheno data from SDRF
Error in .subset2(x, i, exact = exact) : subscript out of bounds

This is a question for Ibrahim Emam, who is the maintainer of ArrayExpress. I would recommend creating a new post with ArrayExpress as a tag so you can be sure Ibrahim sees it.

In general, you don't "make" the CDF file.  Instead, you go back to the array manufacturer and download it.  Someone with more Affy experience might be able to send you a link from the Affy website, but that would be the place to look.