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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 48 minutes ago by
Seyram M.
• 0 • written 4.6 years ago by
hsbio
▴ 10
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 3 hours ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
4
votes
8
replies
295
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 16 hours ago by
Peter Hickey
▴ 740 • written 8 days ago by
Juan Higareda
• 0
0
votes
7
replies
314
views
DESeq filtering specific to contrasts
DESeq2
updated 12 minutes ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
2
votes
5
replies
655
views
DESeq2 setting significant p-value
DESeq2
updated 1 hour ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
6
votes
5
replies
374
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 7 weeks ago by
Kim
• 0
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 18 hours ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
0
votes
4
replies
193
views
DEG with low counts
DESeq2
updated 4 hours ago by
Michael Love
41k • written 4 days ago by
Rajat
• 0
0
votes
4
replies
160
views
FilterByExpr low counts with small sample size
edgeR
1 day ago • updated 3 minutes ago
Jonathan
▴ 10
0
votes
4
replies
74
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
21 hours ago • updated 19 hours ago
sropri
• 0
0
votes
3
replies
68
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 6 hours ago by
Gordon Smyth
50k • written 22 hours ago by
prity6459
• 0
0
votes
3
replies
190
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 23 hours ago by
W. Evan Johnson
▴ 850 • written 7 days ago by
schlumbohm
• 0
0
votes
3
replies
106
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
updated 8 hours ago by
ATpoint
★ 4.0k • written 2 days ago by
lonn
• 0
0
votes
3
replies
37
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 1 hour ago by
James W. MacDonald
65k • written 2 hours ago by
bas_work
▴ 30
1
vote
2
replies
750
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 20 hours ago by
sredemption
• 0 • written 13 months ago by
ruiqi.li
▴ 10
0
votes
2
replies
205
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
18 days ago • updated 1 hour ago
isaac.vock
• 0
0
votes
2
replies
887
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
0
votes
2
replies
45
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
7 hours ago • updated 6 hours ago
prity6459
• 0
1
vote
2
replies
60
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 2 hours ago by
James W. MacDonald
65k • written 18 hours ago by
sansan
• 0
1
vote
2
replies
129
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
1 day ago • updated 19 hours ago
Le
• 0
0
votes
1
reply
44
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 23 hours ago by
Alejandro Reyes
★ 1.9k • written 1 day ago by
Alessia
• 0
0
votes
1
reply
58
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 7 hours ago by
Gordon Smyth
50k • written 1 day ago by
Shaimaa Gamal
• 0
0
votes
0
replies
10
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
58 minutes ago
catv
• 0
0
votes
0
replies
33
views
Warning while loading DEP package
DEP
updated 23 hours ago by
shepherl
3.8k • written 1 day ago by
Namrata
• 0
0
votes
0
replies
23
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
22 hours ago
Mirella Aurora
• 0
1
vote
0
replies
27
views
Tutorial:
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
bioconductor
Install
3 hours ago
BioinfGuru
▴ 30
26 results • Page
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Replies
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
by
isaac.vock
• 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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