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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
18 days ago • updated 17 days ago
Lucy
▴ 60
1
vote
4
replies
250
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
4 weeks ago • updated 29 days ago
samuel.channon
• 0
0
votes
4
replies
194
views
DEG with low counts
DESeq2
updated 8 hours ago by
Michael Love
41k • written 4 days ago by
Rajat
• 0
1
vote
4
replies
398
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 14 days ago by
Gordon Smyth
50k • written 16 days ago by
jari.karppinen
• 0
0
votes
4
replies
2.8k
views
SingleR Label.Ont
SingleR
updated 3 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
0
votes
4
replies
76
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
1 day ago • updated 22 hours ago
sropri
• 0
0
votes
4
replies
180
views
Storing directories inside an ExperimentHub package?
ExperimentHub
9 days ago • updated 8 days ago
Tim Barry
• 0
0
votes
4
replies
117
views
flowStats Search Error
flowStats
updated 3 days ago by
shepherl
3.8k • written 3 days ago by
tholmes
• 0
0
votes
4
replies
281
views
Help with design.matrix
limma
14 days ago • updated 13 days ago
andrea.rodriguez-martinez13
• 0
0
votes
4
replies
360
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
4 weeks ago • updated 24 days ago
Efra
• 0
0
votes
4
replies
169
views
FilterByExpr low counts with small sample size
edgeR
2 days ago • updated 3 hours ago
Jonathan
▴ 10
2
votes
3
replies
273
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 29 days ago by
Michael Love
41k • written 4 weeks ago by
andrebolerbarros
▴ 20
2
votes
3
replies
250
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
4 days ago • updated 3 days ago
daniel.carbajo
• 0
5
votes
3
replies
664
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 22 days ago by
Gordon Smyth
50k • written 29 days ago by
Jack S.
▴ 50
2
votes
3
replies
223
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 24 days ago by
Wei Shi
★ 3.6k • written 25 days ago by
thomas.heigl.ibk
• 0
3
votes
3
replies
259
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
50k • written 11 days ago by
Netanel
• 0
0
votes
3
replies
72
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 9 hours ago by
Gordon Smyth
50k • written 1 day ago by
prity6459
• 0
0
votes
3
replies
107
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
updated 11 hours ago by
ATpoint
★ 4.0k • written 2 days ago by
lonn
• 0
3
votes
3
replies
137
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
7 days ago • updated 1 day ago
jacques.imbert
• 0
1
vote
3
replies
230
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 28 days ago by
Marcel Ramos
690 • written 29 days ago by
Astrid Deschênes
• 0
0
votes
3
replies
2.3k
views
internal error in trio library when trying to use lfmm() in LEA package
lfmm
LEA
updated 26 days ago by
m.charters
• 0 • written 2.9 years ago by
valentinarov
• 0
2
votes
3
replies
313
views
PCA of different bacterial species
DESeq2
updated 23 days ago by
Michael Love
41k • written 23 days ago by
Laura
▴ 10
1
vote
3
replies
220
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 13 days ago by
James W. MacDonald
65k • written 14 days ago by
Shaimaa Gamal
• 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 15 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
1
vote
3
replies
304
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 4 days ago by
Gordon Smyth
50k • written 9 days ago by
Simran
• 0
1
vote
3
replies
245
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 22 days ago by
mercedeh.movassagh
▴ 10 • written 4 weeks ago by
María
• 0
0
votes
3
replies
43
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 4 hours ago by
James W. MacDonald
65k • written 6 hours ago by
bas_work
▴ 30
0
votes
3
replies
190
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 1 day ago by
W. Evan Johnson
▴ 850 • written 7 days ago by
schlumbohm
• 0
3
votes
3
replies
334
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 25 days ago by
alan.ocallaghan
▴ 160 • written 26 days ago by
Najla Abassi
• 0
0
votes
3
replies
307
views
Statistical test
NewWave
written 4 months ago by
mario
• 0
0
votes
3
replies
140
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 3 days ago by
Michael Love
41k • written 4 days ago by
andrebolerbarros
▴ 20
0
votes
2
replies
552
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 25 days ago by
CHEN
• 0 • written 11 months ago by
Saanchi
• 0
0
votes
2
replies
306
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
28 days ago • updated 16 days ago
Gordon
• 0
1
vote
2
replies
208
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
24 days ago
Mj.A.
• 0
1
vote
2
replies
198
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
28 days ago • updated 23 days ago
Chanderkant Chaudhary
• 0
2
votes
2
replies
158
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 14 days ago by
ATpoint
★ 4.0k • written 14 days ago by
Dario Strbenac
★ 1.5k
1
vote
2
replies
85
views
Error in champ.load(): The following specified files do not exist
ChAMP
1 day ago
Sherin
• 0
0
votes
2
replies
192
views
Error in msaFun Cannot open input file. No alignment!
msa
written 4 weeks ago by
Kamil Slowikowski
▴ 30
2
votes
2
replies
1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread
featurecounts
summarizeoverlaps
updated 19 days ago by
isaac.vock
• 0 • written 7.8 years ago by
Jon Manning
▴ 90
1
vote
2
replies
3.0k
views
Extract genes from ggvenn?
ggvenn
updated 14 days ago by
Michael
▴ 10 • written 23 months ago by
axe880
• 0
0
votes
2
replies
888
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
1
vote
2
replies
164
views
How to retrieve detailed regression results from deseq2
DESeq2
8 days ago • updated 23 minutes ago
Weiqian
▴ 10
2
votes
2
replies
336
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
8 days ago • updated 7 days ago
Henry
▴ 10
1
vote
2
replies
190
views
MethylKit read issue
methylKit
updated 13 days ago by
James W. MacDonald
65k • written 19 days ago by
CHEN
• 0
1
vote
2
replies
79
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
3 days ago
Ana
• 0
0
votes
2
replies
261
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
19 days ago • updated 14 days ago
fer_talavera
• 0
0
votes
2
replies
139
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
16 days ago
Marianna
▴ 20
0
votes
2
replies
1.0k
views
error when using M-values in ChAMP
ChAMP
updated 22 days ago by
hortense96
• 0 • written 6.2 years ago by
a.mcneill
• 0
1
vote
2
replies
154
views
Design Matrix within group comparison more than two groups
DESeq2
7 days ago • updated 6 days ago
hemantcnaik
• 0
0
votes
2
replies
871
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 2 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
200 results • Page
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Replies
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
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
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
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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