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Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma
modelmatrix
pairedanalysis
Proteomics
written 9 months ago by
svlachavas
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Comment: DESeq2 for candidate gene analysis
by
piffelpaff
▴ 10
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis
by
Michael Love
43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry
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teamardigen
• 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
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Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Join BOC Sciences at Drug Discovery Chemistry
Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
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