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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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how is `iso_value` transformed to `IF` ? #245

Open sparthib opened 1 month ago

sparthib commented 1 month ago

I have two conditions wherein for condition 1, a given set of isoforms for a gene are not expressed, and iso_value = 0. This in turn gets reported as NaN under IF. Therefore dIF is also reported as NaN. Is there a reason iso_value is transformed to NaN? The set of genes in my samples that are having this issue have evidence of alternate splicing in previous studies, and I would want to see if setting IF = 0 would show any statistically significant dIF. Any pointers or suggestions on how to further analyze this set of genes would be appreciated.

Thanks,

EDIT: I realized this is because for some of these genes, none of their isoforms are being expressed, so gene count (the denominator is 0) therefore leading to NaN values. It would be useful to include these sets of genes in a DTE/DGE analysis however.