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9
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Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 13 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 12 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
4
votes
6
replies
395
views
FilterByExpr low counts with small sample size
edgeR
14 days ago • updated 9 days ago
Jonathan
▴ 10
5
votes
6
replies
413
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 19 days ago by
ATpoint
★ 4.1k • written 22 days ago by
nhaus
▴ 30
0
votes
4
replies
409
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
4 weeks ago • updated 29 days ago
Lucy
▴ 60
1
vote
3
replies
240
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 26 days ago by
James W. MacDonald
65k • written 26 days ago by
Shaimaa Gamal
• 0
1
vote
3
replies
340
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 16 days ago by
Gordon Smyth
50k • written 22 days ago by
Simran
• 0
0
votes
3
replies
168
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 12 days ago by
Gordon Smyth
50k • written 13 days ago by
prity6459
• 0
3
votes
3
replies
313
views
permutation test in edgeR
rna-seq
edgeR
updated 11 days ago by
Gordon Smyth
50k • written 24 days ago by
Netanel
• 0
0
votes
2
replies
155
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
28 days ago
Marianna
▴ 20
0
votes
2
replies
120
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
13 days ago
prity6459
• 0
1
vote
1
reply
158
views
Citation for edgeR user guide
edgeR
updated 8 days ago by
Gordon Smyth
50k • written 8 days ago by
k___
▴ 30
3
votes
1
reply
156
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 13 days ago by
Gordon Smyth
50k • written 14 days ago by
Shaimaa Gamal
• 0
13 results • Page
1 of 1
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Comment: limma-voom: Calculate the log-fold change in gene expression within a sample
by
xofer16091
• 0
A few more names for [dino game][1] are Dino Dun, Chrome Dino, T-Rex, Google, and No Internet games. You can play the online game on a tabl…
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
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…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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