Discrepancies in results between EventPointer R package and TAC4.0

[machalen]

Dear @jpromeror

I am not sure if this is a question I should ask you in issues. I am working for an Affymetrix core facility and we started to use the software Transcriptome Analysis Console (TAC) 4.0 that includes the EventPointer method for alternative splicing analysis. We analyzed Clariom D Affymetrix arrays with TAC and with the R package, and when comparing results there are a lot of discrepancies. When using a cut-off p.value < 0.1 in order to select the events we obtain much more events with the R package. We did a Venn diagram with the intersection of genes containing splicing events, and as you can see there are not many common genes between methods.

Could you tell us which one is the best?

Thank you,

Magda