IPA Core Analysis
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7 weeks ago

Hi,

I had a question concerning the "core analysis" menu of IPA

My RNA-Seq data file is a DESeq2 output file with 26967 genes. In the core analysis of IPA, I only want to analyze differentially expressed genes with a log2FC > 2 for the up-regulated (754 genes) and with a log2FC < 2 for the down-regulated (89 genes). Surprinsingly, when I apply these two cutoffs in the IPA menu (see image), the number of selected genes corresponds only to the up-regulated genes minus 1 (753), the down regulated genes are not taking into account (0 down).
enter image description here I might do something wrong, could you tell me what? Thanks

RNA-Seq • 308 views
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I think only one of those filters applies at one time (either up or down) so you are not doing anything wrong. Create two separate sets. Better yet do the filtering outside IPA and upload the list of genes you want.

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Thanks Genomax. But how is it possible to see up and down-regulated genes on the same pathways?

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Make a list outside IPA and then upload. Or merge the two lists after you filter the genes independently for the core analysis.

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I've done this, but I doesn't work. I still dont' understand why IPA doesn't want to take in consideration my log2FC < -2 genes. I have 843 genes up- and down-regulated, they appear as "Mapped IDs", but only 753 appears as "Analysis ready", even with cutoffs at -2/2 or not....

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That may suggest that IPA is only able to map 753 of the genes in its knowledge base. You must have some predicted genes/pseudo-genes in your list.

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I don't know how to reach the QIAGEN support. Would you have any contact to give me?

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I contacted Qiagen support and will have a meeting on monday about this problem

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