User: longwoodSequencer

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Posts by longwoodSequencer

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Comment: C: regularized log transformation- loss of zero values for sparsely expressed genes
... Thank you Ryan and Michael for your quick responses. I see how negative values are possible in the transformation but that's easier to deal with since that can be interpreted as '<1'. I am bummed about the positive values though. I've uploaded images with an example of this and also a comparison ...
written 2.9 years ago by longwoodSequencer0
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regularized log transformation- loss of zero values for sparsely expressed genes
... I'm using the rlog function in the DESeq2 package and I notice a quirk in the transformed data that I do not know what to make of: for genes that are expressed in a small proportion of samples (say, for gene X, 10 samples have non-zero raw counts out of 300 samples), the transformed dataset has no z ...
deseq2 rlog variancestabilizingtransformation rlog transformation vst written 2.9 years ago by longwoodSequencer0 • updated 2.9 years ago by Michael Love24k

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