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kvittingseerup / IsoformSwitchAnalyzeR

An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
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No gene_q_value or iso_q_value reported #101

Closed jennshah closed 3 years ago

jennshah commented 3 years ago

Hi there,

I imported data from Stringtie using importRdata, then successfully ran IsoformSwitchAnalysisPart1, followed by IsoformSwitchTestDEXSeq, on my SwitchList. The problem is that my results report "NA" for all gene_q_value and iso_q_value fields. All other fields look fine, including isoform_switch_q_value and gene_switch_q_value. Any idea why this might be happening? How should I interpret this? In the switch plots for gene and isoform expression, there do seem to be differences between groups, so I'd like to report q values if they can be generated.

Thanks!

kvittingseerup commented 3 years ago

Hi.

Thanks for reaching out.

The IsoformSwitchTest* functions only identify isoforms switches. You can follow this link to the vignette to see how to add differential expression analysis.

Cheers Kristoffer