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Ashr
•
reset
3
votes
2
replies
1.5k
views
Ashr and IHW
Ashr
LFCShrinkage
IHW
DESeq2
3.2 years ago
Bex
• 0
3
votes
4
replies
1.9k
views
Massive L2FC in DESeq2
deseq2
ashr
rna-seq
4.9 years ago
Alex
• 0
2
votes
2
replies
1.2k
views
Negative svalues from DESeq2 lfcShrink with ashr
ashr
DESeq2
lfcShrink
svalue
4.0 years ago
Enrico
• 0
2
votes
1
reply
1.1k
views
padj NA after shrinking log2FC (DESeq2)
deseq2
ashr
4.5 years ago
da.de
▴ 30
1
vote
5
replies
1.9k
views
lfcShrink probelm in many 0 count genes RNA-seq data
ashr
DESeq2
apeglm
updated 3.5 years ago by
Michael Love
43k • written 3.6 years ago by
Guandong Shang
▴ 40
0
votes
5
replies
2.7k
views
Deseq2, lfcThreshold .
ashr
Deseq2
lfcThreshold
updated 3.5 years ago by
Michael Love
43k • written 4.9 years ago by
Iryna
• 0
0
votes
4
replies
1.0k
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2
apeglm
DESeq
ApeGLM
Ashr
updated 20 months ago by
Michael Love
43k • written 20 months ago by
Ndimensional
▴ 20
0
votes
2
replies
839
views
Ashr error: Optimization failed to converge. Results may be unreliable. Try increasing maxiter and rerunning.
ashr
4.9 years ago
kavator
▴ 30
8 results • Page
1 of 1
Recent ...
Replies
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
by
James W. MacDonald
68k
You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…
Comment: DESeq2 swap ensembl gene id rownames with gene symbol column
by
Erika
• 0
Alternatively, you could have added a column with the common gene names. Assuming your dataframe `df` was created using `DESeq()`, somethin…
Answer: Clarification on GOALL / GO2ALLORFs mapping
by
James W. MacDonald
68k
It appears that 'negative regulation of glycogen biosynthesis' has an 'is a' relationship with 'glycogen biosynthetic process' https://www.…
Comment: Can't post a question?
by
DavideSant
• 0
Thank you, this was super useful!
Comment: Error in retrieving clinical data
by
silickas
• 0
Thank you for the reply. I will try to do that next time. This time instead, I used the GenomicDataCommons package to download clinical dat…
Votes
Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
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