Comments (1)
Hello @ZunpengLiu ,
I don't know if this is still relevant. You can see the issue I opened today as it is related.
I am afraid that if I analyse ERVs separately, I will inadvertently double normalise as DEseq automatically estimates size factors. In order to overcome this, I have passed sizeFactor column set to all 1, so it will normalise but do nothing.
Maybe the best option is what you suggested in point 2 - to not normalise using ERVMap perl script, to concatenate the two matrices and then to go to DEseq where estimateSizeFactors will be called.
If you meanwhile have any more insight into this, please let me know.
from ervmap.
Related Issues (11)
- installation / usage instructions HOT 17
- ERV normalisation questions
- Question about ERV family in ERVmap.bed file
- How was ERVmap.bed generated? HOT 1
- out of order record
- results fileter HOT 5
- Failed to run the jobs
- ERVresults.txt didn't detect any ERVmap HOT 13
- btrim - the requested version (0.3.0) is not available any more HOT 6
- /usr/bin/python2.7 htseq.script.count not found HOT 1
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from ervmap.