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lfcThreshold
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4
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1.3k
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DESeq2 lfcThreshold - all my padj are equal to 1
DESeq2
lfcThreshold
19 months ago
Abir.khazaal
▴ 10
1
vote
2
replies
1.7k
views
DEseq2 anlysis - LfcThreshold and Lfcshrink options
lfcshrink
DESeq2
RNASeq
lfcthreshold
21 months ago
ClaudiaE
• 0
0
votes
5
replies
1.9k
views
Deseq2, lfcThreshold .
ashr
Deseq2
lfcThreshold
updated 2.5 years ago by
Michael Love
41k • written 4.0 years ago by
Iryna
• 0
22
votes
17
replies
7.1k
views
DESeq2 1.20.0 lfcshrink function
deseq2
differential expression
logfoldchange
lfcshrink
lfcthreshold
updated 2.9 years ago by
Michael Love
41k • written 5.8 years ago by
emi.sch
▴ 30
0
votes
1
reply
1.0k
views
DESeq2 - shrunken log fold changes and threshold test
deseq2
lfcshrink
lfcthreshold
differential gene expression
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
corentinrichard374369
• 0
1
vote
2
replies
2.2k
views
[DESeq2] Results summary indicates LFC > and < 0 even with changed lfcThreshold
DESeq2
lfcThreshold
updated 6.1 years ago by
Michael Love
41k • written 6.1 years ago by
Mike
▴ 10
9
votes
2
replies
5.3k
views
log fold change threshold in Deseq2 - using lfcthreshold
lfcthreshold
deseq2
updated 6.3 years ago by
Michael Love
41k • written 6.3 years ago by
lirongrossmann
▴ 80
2
votes
1
reply
3.1k
views
Setting a good lfcThreshold-value in DESeq2 to find stably expressed microRNAs
deseq2
microrna
lfcThreshold
stable expression
ffpe
updated 8.5 years ago by
Michael Love
41k • written 8.5 years ago by
mariakarand
▴ 20
8 results • Page
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Comment: Error in champ.load(): The following specified files do not exist
by
Basti
▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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