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Comment: Check removeBatchEffect effectiveness
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massimo
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Yes, I still get the warning, so there is confounding apparently. However, the resulting adjusted matrix is quite different than before and…
Answer: Limma trend with limpa
by
Gordon Smyth
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Dear Alejandro,
Thanks for your interest.
No, one does not set `trend=TRUE` when running eBayes() after dpcDE(). The variance trends are …
Comment: Check removeBatchEffect effectiveness
by
Gordon Smyth
52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data
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sloperun3az
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0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash
by
sloperun3az
•
0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
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