Differential expression testing while avoiding batch effects due to ambient RNA

MarioniLab / Spermatogenesis2018

Code for Christina and Nils' project to dissect spermatogenesis in mice

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Differential expression testing while avoiding batch effects due to ambient RNA #5

Closed nilseling closed 6 years ago

nilseling commented 6 years ago

@LTLA is a pretty awesome dude! He suggested: Use the log2FC in expression between the empty drops of two conditions as NULL Hypothesis. Test the log2FC obtained from comparisons of the actual groups against the NULL log2FC.

nilseling commented 6 years ago

I now removed genes with logFC > 2 between the ambient profiles and performed DE on the remaining genes (differences in ambient profiles only occur when spermatids are present in one condition but not the other)