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nanoporetech / pipeline-transcriptome-de

Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
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directional fix to the R code; env.yml and config with minor updates #26

Closed sagrudd closed 3 years ago

sagrudd commented 3 years ago

Hei Botond - as discussed in December, here is our agreed fix for the directional flip in the de_analysis.R script - the default behaviour of stringsAsFactors in read_csv has changed; the solution is an explicit stringsAsFactors=TRUE in the import and a reversion to your reversed levels code ... I have touched a version number in the config.yaml (of no consequence but more contemporary pointer to the EMBL dataset) and I have added r-tidyr as a dependency in env.yml that appears to have crept in ...

tested and validated - appears robust

bsipos commented 3 years ago

Thanks! Will merge it ASAP.