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Comment: Research Project - Expanding search funtionality on the GEO database
by
ATpoint
★ 4.2k
Note that GEOquery is inherently limited to array data, are you aware of that? Generally, the problem is with such plans that it would requ…
Answer: Why does DESeq2 give negative log2 fold change in treatment vs control for some
by
Michael Love
42k
If you have other covariates, you can't compare the counts directly. The batch and score influence the expected counts.
Comment: DESeq2 and shrinkage of log2 fold changes
by
Michael Love
42k
It is not enabled by default since 2016. The above post was written before that.
Answer: modelGeneVarByPoisson error selecting bandwidth automatically
by
Peter Hickey
▴ 740
Without a reproducible example or access to the data, it's a bit hard to say. I assume the examples work for you (`example("modelGeneVarBy…
Comment: DESeq2 and shrinkage of log2 fold changes
by
Shannon
• 0
Hi Mike, would you mind clarifying where the lfcShrink is enabled "by default"? As you also mentioned above "The difference between results…
Votes
A: Unable to download "BSgenome.Hsapiens.UCSC.hg19" package using R 3.6.3 on Window
Unable to download "BSgenome.Hsapiens.UCSC.hg19" package using R 3.6.3 on Windows 10 x64
Comment: EnsDb: bad_weak_ptr
DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FUN(X[[i]], ...) : subscript out of bounds" (DEXSeqDataSetFromHTSeq)
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
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