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de
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0
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2
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3.4k
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Using sva ComBat on DESeq2 Data
deseq2
DE
rnaseq
sva
combat
updated 8.2 years ago by
Michael Love
41k • written 8.2 years ago by
mbio.kyle
• 0
2
votes
5
replies
3.2k
views
Possible batch effect correction with RNA-Seq data when the batches do not contain both biological conditions for DE analysis
batch effect
limma
rna seq
DE
updated 4.0 years ago by
Steve Lianoglou
★ 13k • written 4.0 years ago by
svlachavas
▴ 830
2
votes
2
replies
2.7k
views
DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
scRNA-seq
Seurat
DE
updated 4.6 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
ilee8
• 0
5
votes
7
replies
2.2k
views
Alternative tools to perform GO enrichment on DE genes
go
de
enrichment
rnaseq
goana
updated 4.0 years ago by
Gordon Smyth
50k • written 4.0 years ago by
Raito92
▴ 60
3
votes
5
replies
2.1k
views
How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq
rna-seq
filtering
DE
deseq2
updated 4.1 years ago by
Michael Love
41k • written 4.1 years ago by
svlachavas
▴ 830
6
votes
6
replies
2.0k
views
GO enrichment analysis with goana after performing DE analysis with glmTreat
go
DE
edger
rnaseq
glmTreat
updated 4.0 years ago by
Gordon Smyth
50k • written 4.0 years ago by
Raito92
▴ 60
2
votes
7
replies
2.0k
views
Limma analysis with multiple variables
limma
model.matrix
de
design
rnaseq
updated 3.9 years ago by
Gordon Smyth
50k • written 3.9 years ago by
Will
• 0
7
votes
13
replies
1.8k
views
Taking into account strong batch effect in microarray differential expression analysis with limma
limma
microarray
hugeneST
batch effect
DE
updated 5.3 years ago by
Ryan C. Thompson
★ 7.9k • written 5.3 years ago by
svlachavas
▴ 830
1
vote
5
replies
1.7k
views
Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2
DE
DEG
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
hermanapis
• 0
0
votes
5
replies
1.7k
views
DESeq2 for DE analysis in developmental stages of tomato pollen
DESeq2
DE
normalization
6.7 years ago
mario.keller.1988
▴ 20
1
vote
2
replies
1.7k
views
Error message running DE-test in Monocle
monocle
cummerbund
DE
rnaseq
updated 8.8 years ago by
ksekine
• 0 • written 9.0 years ago by
Jon Bråte
▴ 250
3
votes
3
replies
1.4k
views
Different number of marker genes between same clusters
sce
markers
single cell
DE
clusters
4.6 years ago
ludmi.b
• 0
3
votes
4
replies
1.3k
views
Paired analysis (tumor vs normal) at three different conditions with EdgeR
edger
design
matrix
de
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
takumima
▴ 10
3
votes
5
replies
1.2k
views
Different numbers of DE genes using edgeR and DESEQ2
edger
deseq2
rnaseq
de
updated 4.0 years ago by
Gordon Smyth
50k • written 4.0 years ago by
Raito92
▴ 60
0
votes
2
replies
1.2k
views
coef for limma differential expression analysis
limma
DE
updated 7.2 years ago by
svlachavas
▴ 830 • written 7.2 years ago by
Dave
• 0
0
votes
3
replies
983
views
DESeq2 - nested samples (individuals) - time course - conditions
deseq2
nested
de
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
gaio.transposon
• 0
0
votes
1
reply
945
views
Interactions and contrasts for DE analysis in ballgown
ballgown
R
RNAseq
DE
interactions
updated 5.8 years ago by
James W. MacDonald
65k • written 5.8 years ago by
khill33
• 0
0
votes
1
reply
908
views
Multi-level experiment with continuous varibles and confounders in limma
limma
de
differential gene expression
multi-tissue design
multi-level design
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
kdiamanti
• 0
1
vote
1
reply
629
views
different observation of DEG for same group
deseq2
DE
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
lkianmehr
• 0
19 results • Page
1 of 1
Recent ...
Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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