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edgeR
•
reset
2
votes
1
reply
1.0k
views
Error in `rownames<-`(`*tmp*`, value = list(genes
edger
updated 8.1 years ago by
Aaron Lun
★ 29k • written 8.1 years ago by
mictadlo
▴ 10
5
votes
4
replies
1.9k
views
Differential expression analysis desgin
differential expression
deseq2
edger
interactions
limma
updated 8.1 years ago by
Gordon Smyth
53k • written 8.1 years ago by
kendralec
▴ 10
2
votes
1
reply
1.1k
views
combine two differential expression methods
edger
deseq2
dea
publish
updated 8.1 years ago by
Aaron Lun
★ 29k • written 8.1 years ago by
roser.navarro
• 0
2
votes
4
replies
1.7k
views
Removing batch effect on edgeR when interactons are looked at
rnaseq
edger
statistics
model matrix
updated 8.1 years ago by
Steve Lianoglou
★ 13k • written 8.1 years ago by
David R
▴ 90
2
votes
1
reply
1.2k
views
edgeR normalisation which samples to include
edger
normalization
samples
comparisons
updated 8.1 years ago by
Gordon Smyth
53k • written 8.1 years ago by
roser.navarro
• 0
0
votes
3
replies
1.8k
views
Differential expression of individual genes using edgeR
edger
differential gene expression
8.1 years ago
fawazfebin
▴ 60
26
votes
7
replies
13k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma
deseq2
edger
rnaseq
updated 8.1 years ago by
Gordon Smyth
53k • written 8.2 years ago by
Jack
▴ 20
4
votes
9
replies
3.1k
views
tximport recommendation for limma-trend downstream analysis?
tximport
limma
limma-trend
edgeR
updated 8.2 years ago by
Aaron Lun
★ 29k • written 8.2 years ago by
Jenny Drnevich
★ 2.0k
4
votes
2
replies
1.6k
views
Differential gene expression for multi-factorial experiment using edgeR
edger
differential gene expression
multiple factor design
updated 8.2 years ago by
Aaron Lun
★ 29k • written 8.2 years ago by
akulkarn
• 0
1
vote
2
replies
3.8k
views
DESeq2/edgeR DEG analysis data input from TCGA and correation analysis
edgeR
TCGA
updated 8.2 years ago by
Aaron Lun
★ 29k • written 8.2 years ago by
JackieMe
• 0
4
votes
6
replies
2.2k
views
EdgeR: Replicate samples diverge in MDS plot
edger
plotmds
8.2 years ago
fawazfebin
▴ 60
3
votes
1
reply
2.5k
views
column nubering plotMDS
edger
plotmds
updated 8.2 years ago by
Aaron Lun
★ 29k • written 8.2 years ago by
mictadlo
▴ 10
10
votes
14
replies
5.9k
views
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma
edger
deseq
deseq2
updated 8.2 years ago by
Gordon Smyth
53k • written 8.2 years ago by
Nik Tuzov
▴ 90
10
votes
6
replies
5.5k
views
Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq
deseq2
edger
voom
limma
updated 8.2 years ago by
Paul Harrison
▴ 110 • written 10.5 years ago by
Sean Davis
21k
0
votes
1
reply
920
views
differentially expressed genes form RSEM genes data
rnaseq
edgeR
updated 8.2 years ago by
Gordon Smyth
53k • written 8.2 years ago by
lily
▴ 20
0
votes
3
replies
3.2k
views
topGO - missing value where TRUE/FALSE needed
topgo
edger
8.2 years ago
mictadlo
▴ 10
3
votes
3
replies
1.3k
views
Saving output from glmTreat to a csv file?
edger
rna-seq
updated 8.2 years ago by
Aaron Lun
★ 29k • written 8.2 years ago by
mictadlo
▴ 10
1
vote
1
reply
1.8k
views
Does edgeR accept decimal / integer read counts for differential expression ?
edger
differential gene expression
updated 8.2 years ago by
Gordon Smyth
53k • written 8.2 years ago by
Padhmanand.Sudhakar
• 0
8
votes
3
replies
2.6k
views
Why edgeR::aveLogCPM() is simlar to log2(rowMeans(cpm)) instead of rowMeans(cpm(y, log=TRUE))
edgeR
rnaseq
limma
independent filtering
8.2 years ago
Robert Castelo
★ 3.4k
0
votes
2
replies
2.0k
views
bias.data vector must have the same length as DEgenes vector!
edger
goseq
updated 8.2 years ago by
Aaron Lun
★ 29k • written 8.2 years ago by
mictadlo
▴ 10
3
votes
1
reply
687
views
adding genes to edgeR
edger
updated 8.2 years ago by
Aaron Lun
★ 29k • written 8.2 years ago by
mictadlo
▴ 10
0
votes
3
replies
2.0k
views
goseq after edgeR
edger
goseq
updated 8.2 years ago by
Aaron Lun
★ 29k • written 8.2 years ago by
mictadlo
▴ 10
0
votes
2
replies
1.7k
views
how to build gene.pathway data.frame for non-model organism
limma
kegg
topgo
dataframe
edger
8.2 years ago
mictadlo
▴ 10
2
votes
4
replies
1.7k
views
differentially expressed miRNA using edge R
edger
updated 8.2 years ago by
Gordon Smyth
53k • written 8.2 years ago by
lily
▴ 20
2
votes
2
replies
2.9k
views
plotMD plot change plot title
edger
plotmd
updated 8.2 years ago by
Gordon Smyth
53k • written 8.2 years ago by
mictadlo
▴ 10
0
votes
5
replies
3.4k
views
How to use topGO and KEGG with de-novo species
topgo
edger
limma
kegga
kegg
updated 8.2 years ago by
Gordon Smyth
53k • written 8.2 years ago by
mictadlo
▴ 10
3
votes
3
replies
1.1k
views
Examples of concise description of NGS and bioinformatics (with DESEq2 or edgeR) in M&M of biological paper
deseq2
edgeR
updated 8.2 years ago by
Gordon Smyth
53k • written 8.2 years ago by
Vladimir Krasikov
▴ 90
1
vote
2
replies
5.2k
views
Length of 'group' must equal number of columns in 'counts'
htseqcounts
edger
updated 3.1 years ago by
Randy
• 0 • written 8.2 years ago by
mictadlo
▴ 10
3
votes
7
replies
3.9k
views
read counts for each gene for edgeR
edger
htseqcounts
updated 8.2 years ago by
Gordon Smyth
53k • written 8.2 years ago by
mictadlo
▴ 10
2
votes
3
replies
3.7k
views
plotMDS axis labels for limma/EdgeR: PCA or PCoA
limma
edgeR
updated 8.2 years ago by
Gordon Smyth
53k • written 8.2 years ago by
andrew.lonsdale
• 0
2
votes
2
replies
1.2k
views
DESeq2 comparing differential expression results
deseq2
edger
updated 8.2 years ago by
Michael Love
43k • written 8.2 years ago by
rrcutler
▴ 70
11
votes
15
replies
3.8k
views
edgeR - MDS Plot for Count Data
edger
DEG
mds
plot
8.3 years ago • updated 8.2 years ago
baus87
• 0
1
vote
2
replies
1.1k
views
normalization of POL2 ChIP-seq for the calculation of POL2 Pausing Ratios
edgeR
deseq2
normalization
updated 8.2 years ago by
Aaron Lun
★ 29k • written 8.2 years ago by
Bogdan
▴ 670
1
vote
13
replies
3.4k
views
Why Differential expression results differ with edgeR and limma ?
limma
edgeR
differential gene expression
r
8.3 years ago
Biologist
▴ 120
2
votes
9
replies
2.4k
views
decideTests error with edgeR package
edger
r
differential gene expression
updated 8.3 years ago by
Aaron Lun
★ 29k • written 8.3 years ago by
Biologist
▴ 120
4
votes
4
replies
2.0k
views
edgeR design between and within subjects
edgeR
design and contrast matrix
updated 8 months ago by
wuwenhui2
• 0 • written 8.3 years ago by
b.nota
▴ 370
3
votes
3
replies
8.9k
views
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq
rna-seq
limma
geoquery
edger
updated 8.3 years ago by
Sean Davis
21k • written 8.3 years ago by
hkarakurt
▴ 20
3
votes
1
reply
1.9k
views
Filtering step in Differential analysis with RSEM values
rsem
differential gene expression
edger
updated 8.3 years ago by
Gordon Smyth
53k • written 8.3 years ago by
Biologist
▴ 120
3
votes
1
reply
1.5k
views
Common dispersion value using edgeR for DEGs analysis
edgeR
DEGS
common disperion
updated 8.3 years ago by
Aaron Lun
★ 29k • written 8.3 years ago by
baus87
• 0
4
votes
8
replies
2.8k
views
Advice regarding RNAseq data with no replicates, best approach to accomplish fold-change
rnaseq
edger
DGE
no replicates
8.3 years ago
Stefany Solano
• 0
1
vote
1
reply
1.7k
views
edgeR change first column to row name
edger
tibble
updated 8.3 years ago by
Aaron Lun
★ 29k • written 8.3 years ago by
jattnicole29
• 0
2
votes
14
replies
9.7k
views
Calculating rpkm from counts data?
r
featurecounts
rpkm
tpm
edger
updated 2.7 years ago by
Chris
▴ 20 • written 8.3 years ago by
Biologist
▴ 120
1
vote
9
replies
2.4k
views
edgeR in a situation with unbalanced design: to include only subjects with matching time points or not?
edgeR
differential gene expression
updated 8.3 years ago by
Gordon Smyth
53k • written 8.3 years ago by
cafelumiere12
▴ 20
1
vote
1
reply
2.3k
views
limma: The topTable function implementation when outputin the differential expression results from RNA-seq dataset?
limma
voom
edgeR
toptable
output
updated 8.3 years ago by
Aaron Lun
★ 29k • written 8.3 years ago by
heikki.sarin
▴ 10
4
votes
8
replies
2.9k
views
edgeR: How to set model for glmQLFTest in time-course experiment (compared to glmLRT?
edgeR
edger "glmqlftest()"
timecourse
model
updated 8.3 years ago by
Ryan C. Thompson
★ 7.9k • written 8.3 years ago by
heikki.sarin
▴ 10
3
votes
11
replies
3.2k
views
Exporting normalized counts over final DB windows from csaw
csaw
edger
chip-seq
updated 8.3 years ago by
Ryan C. Thompson
★ 7.9k • written 8.3 years ago by
jms1223
▴ 10
0
votes
16
replies
2.5k
views
edgeR DE gene calculation problem
edgeR
updated 8.3 years ago by
Aaron Lun
★ 29k • written 8.3 years ago by
jw24
• 0
1
vote
3
replies
2.3k
views
edgeR and lack of counts ID on CPM matrix
edgeR
8.3 years ago
abrantes.patricia
▴ 10
1
vote
8
replies
2.2k
views
EdgeR model not of full rank
EdgeR
rank
model
8.4 years ago • updated 8.3 years ago
philip.freda
• 0
2
votes
4
replies
1.4k
views
Adjusting for procedural effect
edger
8.4 years ago
elineverbon
▴ 20
2,031 results • Page
19 of 41
Recent ...
Replies
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions. First, I examined th…
Answer: Finding duplicated entries in GRangesList
by
Kevin Blighe
★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data
by
Kevin Blighe
★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed.
by
Kevin Blighe
★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot
by
Kevin Blighe
★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
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