How convert probe ids between different Affymetrix chips for Arabidopsis Thaliana

Question

[eisa_kohan]

Dear all,

I start working in system biology. I have some problem for dataset analysis. I have two different microarray data from two different affymetrix chip. I need to compare data together, and how could I matc them? each data has special prob Id. How could I convert one of them to another??

thanks a lot

Answer 1

[simon.pearce]

(this question should not be in Chip-Seq, this is Microarrays)

Which Arabidopsis Affymetrix chips are you trying to compare between? You probably need to find a table for each which maps probe ID to AGI code (gene ID) for both chips. For the ATH chip, I use a table I downloaded from TAIR (somewhere in the bulk data download ftp server) a long time ago, affy_ATH1_array_elements-2010-12-20.txt, and then I have a function written in R to convert lists.

Alternatively, you if only have a few lists you can use an online converter, for instance the one at the eFP browser, http://bar.utoronto.ca/welcome.htm .

Some more information may help.