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edger
•
reset
0
votes
0
replies
33k
views
Why the resuts are so different between the classic and the glm methods?
edgeR
edgeR
10.3 years ago
Jiantao Yu
▴ 10
18
votes
4
replies
32k
views
FDR and padj in deseq and edger
deseq2
edger
updated 8.4 years ago by
Gordon Smyth
50k • written 8.4 years ago by
tonja.r
▴ 80
17
votes
4
replies
30k
views
RPKM, CPM and TMM
edger
rnaseq
differential expression
updated 8.7 years ago by
Aaron Lun
★ 28k • written 8.7 years ago by
Pauly Lin
▴ 150
15
votes
6
replies
29k
views
How does edgeR cpm function calculate log(CPM) values?
edgeR
cpm
updated 5.8 years ago by
ftroot1010
▴ 20 • written 6.0 years ago by
jxb.dev
▴ 40
3
votes
12
replies
23k
views
P Value of 0?
differential gene expression
edger
updated 9.1 years ago by
Matthew McCormack
▴ 180 • written 9.1 years ago by
dsperley
• 0
0
votes
1
reply
21k
views
Error in .External.graphics(C_layout, num.rows, num.cols, mat, as.integer(num.figures)
edger
ggplot
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
mictadlo
▴ 10
4
votes
4
replies
20k
views
edgeR rpkm function
edger
rpkm
updated 12 months ago by
Gordon Smyth
50k • written 9.2 years ago by
Makis Motakis
▴ 30
1
vote
4
replies
20k
views
edgeR: non-unique values when setting 'row.names' - but the row names are unique!!!
edgeR
row.names
DGEList
9.1 years ago
ccheung
• 0
13
votes
11
replies
17k
views
edgeR TMM values
edger
8.2 years ago
ribioinfo
▴ 100
21
votes
13
replies
16k
views
Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
edger
rnaseq
updated 9.4 years ago by
James W. MacDonald
65k • written 9.4 years ago by
candida.vaz
▴ 50
3
votes
2
replies
16k
views
how to calculate gene length to be used in rpkm() in edgeR
RNASeq
edgeR
rpkm
updated 11 months ago by
Gordon Smyth
50k • written 9.9 years ago by
shirley zhang
★ 1.0k
0
votes
2
replies
15k
views
EdgeR LogCpm and LogFC values calculation
edgeR
edgeR
updated 10.2 years ago by
Koen Van den Berge
▴ 180 • written 10.2 years ago by
Gordon Smyth
50k
7
votes
3
replies
15k
views
edgeR normalization method
edgeR
differential expression
normalization
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
Sara
▴ 10
4
votes
7
replies
14k
views
package ‘edgeR’ is not available (for R version 3.1.2)
edgeR
packages
9.1 years ago
Patrick Schorderet
▴ 20
6
votes
4
replies
14k
views
EdgeR Design matrix not of full rank
edger
updated 8.8 years ago by
Gordon Smyth
50k • written 8.8 years ago by
kjclowers
• 0
13
votes
20
replies
13k
views
Can I feed TCGA normalized count data to EdgeR for differential gene expression analysis
EdgeR
TCGA
normalized count
updated 9.0 years ago by
alakatos
▴ 130 • written 9.0 years ago by
ycding
▴ 10
0
votes
9
replies
13k
views
edgeR warnings and then error
edgeR
edgeR
updated 11.4 years ago by
Gordon Smyth
50k • written 11.4 years ago by
john herbert
▴ 560
0
votes
7
replies
13k
views
Applying DESeq on RSEM output
edgeR
DESeq
edgeR
DESeq
updated 3.0 years ago by
mehdimerbah
• 0 • written 11.0 years ago by
dvir.tau@gmail.com
▴ 30
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 21 months ago by
Mohamed
▴ 30
0
votes
1
reply
12k
views
Error in colSums(counts) : 'x' must be numeric
edgeR
edgeR
updated 12.6 years ago by
Vincent J. Carey, Jr.
6.7k • written 12.6 years ago by
Khan, Saad M. MU-Student
▴ 10
13
votes
11
replies
11k
views
RNA-Seq, generate batch-free count matrix
edgeR
sva
updated 9.4 years ago by
Gordon Smyth
50k • written 9.7 years ago by
Brian Haas
▴ 90
25
votes
37
replies
11k
views
Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
rnaseq
RSEM
TCGA
edgeR
normalization
updated 7.2 years ago by
Gordon Smyth
50k • written 7.2 years ago by
svlachavas
▴ 830
6
votes
6
replies
10k
views
Why different filtering criteria using CPM to filter the RNA-seq count data in edgeR have so much influence on the number of DE genes?
rnaseq
edger
6.4 years ago
Jack
• 0
8
votes
5
replies
10k
views
EdgeR glmLRT vs glmQLFTest
bioconductor
edger
updated 7.8 years ago by
Steve Lianoglou
★ 13k • written 7.8 years ago by
grastalt27
• 0
3
votes
2
replies
10k
views
Batch effect removal in edgeR
edger
batch effect
updated 9.2 years ago by
Gordon Smyth
50k • written 9.2 years ago by
candida.vaz
▴ 50
2
votes
1
reply
9.9k
views
How can I get the normalized read counts from TMM?
Normalization
edgeR
Normalization
edgeR
updated 11.5 years ago by
Mark Robinson
▴ 880 • written 11.5 years ago by
Reanne Bowlby
▴ 20
3
votes
11
replies
9.9k
views
How to interpret plotBCV plots in edgeR
rnaseq
edger
7.1 years ago
davide.bau
• 0
5
votes
7
replies
9.9k
views
threshold to filter lowly expressed genes
edger
rnaseq
updated 10 weeks ago by
Shaimaa Gamal
• 0 • written 7.0 years ago by
myprogramming2016
• 0
0
votes
4
replies
9.8k
views
edgeR: Value of variation of biological variation (BCV)
edgeR
edgeR
updated 11.6 years ago by
Gordon Smyth
50k • written 11.6 years ago by
KJ Lim
▴ 420
11
votes
10
replies
9.4k
views
How to determine which edgeR glmFit and glmQLFit are better
edger
updated 8.2 years ago by
Gordon Smyth
50k • written 8.2 years ago by
changjiang.h.xu
▴ 10
21
votes
7
replies
9.3k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma
deseq2
edger
rnaseq
updated 6.5 years ago by
Gordon Smyth
50k • written 6.5 years ago by
Jack
• 0
8
votes
11
replies
9.3k
views
Filtering of RNA-seq data in EdgeR
rnaseq
edger
filtering
updated 7.7 years ago by
David ROUX
▴ 20 • written 7.8 years ago by
alireza_sharifian_10
▴ 10
4
votes
4
replies
8.6k
views
Filtering read counts matrix: how to deal with duplicated gene symbols, different ENSEMBL ids
edger
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
es874
▴ 20
8
votes
12
replies
8.5k
views
EdgeR: Explaning dispersion types to newbies
edger
dispersion
estimatedispersions
visualization
teaching
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
Mr.RB
▴ 20
3
votes
4
replies
8.4k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 8 weeks ago by
Dimitris
• 0 • written 10.8 years ago by
Makis Motakis
▴ 30
0
votes
2
replies
8.3k
views
edgeR vs DESeq for comparison without replicate
edgeR
DESeq
edgeR
DESeq
updated 12.7 years ago by
Davis McCarthy
▴ 260 • written 12.7 years ago by
Woo, Sangsoon
▴ 20
7
votes
18
replies
8.2k
views
Differential expression analysis: Continuous variables
DESeq
EdgeR
limma
8.5 years ago
Radek
▴ 90
6
votes
6
replies
8.0k
views
EdgeR design matrix with 3 factors
edger
glm
rnaseq
6.3 years ago
Denniswu
▴ 20
19
votes
4
replies
8.0k
views
Confidence intervals on edgeR logFC
edgeR
statistics
confidence interval
updated 8.0 years ago by
nwvidal
• 0 • written 9.5 years ago by
ri.lars
▴ 40
4
votes
4
replies
8.0k
views
edgeR design matrix and contrasts: how to make contrast between groups that aren't shown in the design matrix columns?
edger
design and contrast matrix
contrast
limma contrast matrix
limma
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
cafelumiere12
▴ 20
3
votes
3
replies
7.9k
views
TPM data Differential expression analysis
edger
limma
differential gene expression
updated 22 months ago by
Gordon Smyth
50k • written 5.9 years ago by
ghmdsr
• 0
3
votes
9
replies
7.9k
views
edgeR and batch effect
edger
updated 6.3 years ago by
sutturka
• 0 • written 6.8 years ago by
abrantes.patricia
▴ 10
3
votes
5
replies
7.7k
views
DESeq2 vs edgeR results analysis
deseq2
edgeR
updated 2.2 years ago by
Gordon Smyth
50k • written 3.9 years ago by
adR
▴ 30
25
votes
11
replies
7.7k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq
deseq2
edgeR
normalization
updated 8.4 years ago by
Simon Anders
★ 3.7k • written 8.4 years ago by
Nik Tuzov
▴ 80
5
votes
12
replies
7.7k
views
Remove batch effect in small RNASeq study (SVA or others?)
RNASeq
Alignment
edgeR
sva
updated 9.2 years ago by
Gordon Smyth
50k • written 9.9 years ago by
shirley zhang
★ 1.0k
9
votes
11
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 8.7 years ago by
Gordon Smyth
50k • written 8.7 years ago by
gthm
▴ 30
12
votes
13
replies
7.6k
views
EdgeR Differential Expression analysis with NAs
EdgeR
rnaseq
NA
updated 9.5 years ago by
Aaron Lun
★ 28k • written 9.5 years ago by
elliott77
• 0
2
votes
2
replies
7.6k
views
edgeR: How is FDR calculated for logFC? (False Discovery Rate)
edgeR
bioconductor
fdr
statistics
differential gene expression
7.3 years ago
jol.espinoz
▴ 40
21
votes
1
reply
7.5k
views
Differences between limma voom E values and edgeR cpm values?
edgeR
updated 9.5 years ago by
Gordon Smyth
50k • written 9.8 years ago by
John Brothers II
▴ 90
6
votes
5
replies
7.5k
views
how to understand cpm=1 and how filterByExpr works?
edger
updated 22 months ago by
gowthamee
▴ 10 • written 3.6 years ago by
linouhao
▴ 20
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Comment: fgsea fork
by
Sofa
• 0
Workshops and summer schools offer immersive learning experiences outside traditional academic settings, catering to diverse interests and …
Comment: limma models out of memory issue on Slurm HPC
by
SamGG
▴ 330
> Alternatively you could run each linear model fit (var1 to var6) in a separate batch run, and again that would presumably work. I think …
Comment: fgsea fork
by
shepherl
3.8k
For What its worth BiocManager should also be able to install the github remotes `BiocManager::install("ctlab/fgsea")`
Comment: fgsea fork
by
alserg
▴ 240
I'm also not sure what you mean by fork, but you also can install the latest version of fgsea directly from GitHub with `devtools::install_…
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
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transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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