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lfcShrink
•
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0
votes
4
replies
690
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Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink
DESeq2
written 4 months ago by
Igor
• 0
2
votes
17
replies
1.8k
views
lfcshrink error DESeq2
DESeq2
lfcshrink
DESe
updated 12 months ago by
Michael Love
42k • written 12 months ago by
Alina
• 0
3
votes
4
replies
879
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
9 months ago
Eva
▴ 10
4
votes
4
replies
826
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
10 months ago
bhandary.8590
▴ 20
1
vote
1
reply
2.3k
views
Question regarding lfcShrink types in DiffBind
FoldChange
DiffBind
lfcShrink
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
bhandary.8590
▴ 20
0
votes
2
replies
535
views
DESeq2 : stat or lfcshrink for GSEA analysis
lfcshrink
GSEABenchmarkeR
DESeq2
updated 5 months ago by
ATpoint
★ 4.1k • written 5 months ago by
delphine.rossille
• 0
6 results • Page
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Comment: Extremely small p-values using Limma for proteomic data
by
Robert Castelo
★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Comment: deseq2 results
by
ATpoint
★ 4.1k
> the results are not satisfactory to me Well, what is your question? The DESeq2 vignette covers how to do analysis, and some diagnostics…
Comment: Extremely small p-values using Limma for proteomic data
by
ATpoint
★ 4.1k
It's not an implementation problem I am discussing (it's trivial obviously) -- more that for most purposes the y-axis metric should be the …
Comment: Extremely small p-values using Limma for proteomic data
by
Robert Castelo
★ 3.3k
For visualization purposes you can draw an horizontal line at the p-value cutoff that meets the experiment-wide FDR cutoff. For instance, i…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Ask yourself the question how a gene that is exactly the same everywhere adds anything to any analysis. Heatmaps usually take DEGs to infer…
Votes
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
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