finding microarray probesets orientation: sense or antisense

Question

[hosseinkhan]

Dear all,

I need to obtain microarray probesets orientations. I downloaded the corresponding probe IDs from affymetrix but the orientation of all 77674 probes has been recorded as antisense while this is not true for the annotation file. The reason that I can not use the annotation file is that he orientation of only one third of probes are available.

Do anyone knows about the observed discrepancy between these two files and what should I do to get the orientation of all probes?

Thanks in advance

Nazanin

[Devon Ryan]

That's really annoying. Which of the Affymetrix chips is this? You might get lucky and find that the annotation package from Bioconductor is complete.

[hosseinkhan]

Hi, I encountered this problem with S.aureus and P.aeruginosa probe IDs obtained from product page of affymetrix. as an input for an algorithm I need the start and end position of each probe on the reference genome beside their orientation, i.e. plus or minus. Since this information are not provided for all probes in annotation file, I tried their corresponding probeIDs files, but the orientation of all probes have been recorded as antisense. I would be grateful if you guide me. Thanks

PhD candidate of Bioinformatics, Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran