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ashr
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3
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4
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1.5k
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Massive L2FC in DESeq2
deseq2
ashr
rna-seq
4.0 years ago
Alex
• 0
2
votes
2
replies
1000
views
Ashr and IHW
Ashr
LFCShrinkage
IHW
DESeq2
2.4 years ago • updated 2.3 years ago
Bex
• 0
2
votes
1
reply
884
views
padj NA after shrinking log2FC (DESeq2)
deseq2
ashr
3.6 years ago
da.de
▴ 30
2
votes
2
replies
899
views
Negative svalues from DESeq2 lfcShrink with ashr
ashr
DESeq2
lfcShrink
svalue
3.2 years ago • updated 3.1 years ago
Enrico
• 0
1
vote
5
replies
1.4k
views
lfcShrink probelm in many 0 count genes RNA-seq data
ashr
DESeq2
apeglm
updated 2.7 years ago by
Michael Love
41k • written 2.7 years ago by
Guandong Shang
▴ 40
0
votes
5
replies
2.0k
views
Deseq2, lfcThreshold .
ashr
Deseq2
lfcThreshold
updated 2.6 years ago by
Michael Love
41k • written 4.0 years ago by
Iryna
• 0
0
votes
2
replies
630
views
Ashr error: Optimization failed to converge. Results may be unreliable. Try increasing maxiter and rerunning.
ashr
4.0 years ago
kavator
▴ 30
0
votes
4
replies
653
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2
apeglm
DESeq
ApeGLM
Ashr
updated 9 months ago by
Michael Love
41k • written 9 months ago by
Ndimensional
▴ 20
8 results • Page
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Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Votes
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
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