What is the best approach to analyze RNA-seq data over 3 time points, but with average 60% missing samples in different time points?
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@e4025bc7
Last seen 7 weeks ago
United States

My dataset is something like:

t1: 40 samples (8 also participate in t2, 6 in t3) t2: 10 samples t3: 7 samples

This implies many participants (samples) are missing in different timepoints.

RNASeq • 102 views
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@james-w-macdonald-5106
Last seen 2 hours ago
United States

In general, when you have repeated measures for some but not all of your subjects, you would use a linear mixed model. To do that using edgeR/limma you would use the voomLmFit function, blocking on subject (e.g., you would provide a factor of the subjects to the block argument).