Affymetrix cross platform probe matching

Question

[gracie]

Hi all,

I have multiple datasets some from hgu133plus2 ( GPL570) and one affymetrix human exon array 1.0st. I wanna compare the DEGs from these two platforms. Is there any cross platform probe matching data for affymetrix or any suggestions to deal with multiple probesets hitting same gene problem?

Thanks in advance

Answer 1

[Kevin Blighe]

Hello, can you please elaborate on what you mean by 'compare'? - do you mean to merge the datasets or to perform a meta-analysis?

[gracie]

Clustering based on DEGs basicly and also extracting the genes altered same and opposite direction. I am not planing to do meta analysis because each dataset contains their own control group and I am only intrested in DEGs.

[Kevin Blighe]

Okay, I would convert the probe identifiers to a common annotation type and then go by that. For example, convert to HGNC symbols or Ensembl gene IDs.