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Rank
Views
Votes
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
14 days ago • updated 3 days ago
Chris
• 0
14
votes
4
replies
29k
views
heatmap.2() get matrix after hierarchical clustering
Clustering
Clustering
updated 11.6 years ago by
Thomas Girke
★ 1.7k • written 11.6 years ago by
Guest User
★ 13k
14
votes
5
replies
22k
views
Dealing with genes that have Padj=NA
deseq2
updated 9 months ago by
Juan Pablo
• 0 • written 8.4 years ago by
raya.fai
▴ 60
14
votes
12
replies
9.3k
views
limma lmFit coefficients and p-values
limma
methylation
ewas
updated 7.8 years ago by
Steve Lianoglou
★ 13k • written 7.8 years ago by
CPR
▴ 30
14
votes
8
replies
2.6k
views
News:
Bioconductor packages now each have a DOI.
doi
citation
News
updated 6.7 years ago by
Martin Morgan
25k • written 6.7 years ago by
Sean Davis
21k
14
votes
1
reply
2.0k
views
it paused in line **byte-compile and prepare package for lazy loading** when install package EnsDb.Hsapiens.v75
EnsDb.Hsapiens.v75
updated 3.3 years ago by
Batool
▴ 370 • written 3.4 years ago by
YunYun
▴ 70
14
votes
19
replies
8.9k
views
DESeq2 Model Design
DESeq2
linear model
model
updated 3.0 years ago by
Michael Love
41k • written 9.4 years ago by
andrew.j.skelton73
▴ 370
14
votes
9
replies
3.8k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma
rna-seq
removebatcheffect()
updated 6.3 years ago by
alakatos
▴ 130 • written 8.0 years ago by
Ekarl2
▴ 80
14
votes
16
replies
2.6k
views
Limma - discrepancy in number of significant genes
limma
differential gene expression
microarray
linear model
updated 8.9 years ago by
James W. MacDonald
65k • written 8.9 years ago by
bcbio_uk
▴ 10
14
votes
10
replies
4.8k
views
HDF5 reading speed
rhdf5
hdf5
updated 6.2 years ago by
Mike Smith
★ 6.5k • written 6.2 years ago by
felicien.meunier
▴ 40
14
votes
4
replies
14k
views
WGCNA Hub Gene Selection Method
WGCNA
Hub Genes
KmE
Intramodular Connectivity
updated 8.8 years ago by
Peter Langfelder
★ 3.0k • written 8.8 years ago by
brohawndg
▴ 150
13
votes
10
replies
3.9k
views
Big differences in logfoldchange for some genes between edgeR and DESeq2
edger
deseq2
updated 8.4 years ago by
Gordon Smyth
50k • written 8.4 years ago by
Matarit
• 0
13
votes
6
replies
6.2k
views
goana limma- extract list of DE genes and genes in the enriched GO terms?
limma
goana
updated 8.8 years ago by
Gordon Smyth
50k • written 8.8 years ago by
carl.mann
▴ 20
13
votes
3
replies
12k
views
Understanding contrasts limma
limma
design and contrast matrix
updated 8.6 years ago by
Aaron Lun
★ 28k • written 8.6 years ago by
Andy91
▴ 60
13
votes
12
replies
6.6k
views
From a ENST to ENSG
AnnotationDbi
3.3 years ago
suxxa
▴ 20
13
votes
1
reply
2.9k
views
News:
Updated Bioconductor Package Submission Policy
package
submission
News
8.3 years ago
Martin Morgan
25k
13
votes
20
replies
14k
views
Can I feed TCGA normalized count data to EdgeR for differential gene expression analysis
EdgeR
TCGA
normalized count
updated 9.1 years ago by
alakatos
▴ 130 • written 9.1 years ago by
ycding
▴ 10
13
votes
5
replies
7.1k
views
EDGE-R exact test vs QL F-test
edger
rnaseq
updated 2.0 years ago by
Sarah
• 0 • written 7.9 years ago by
kaihami
▴ 30
13
votes
6
replies
7.1k
views
DESeq2 multiple interaction terms 3-factor design
deseq2
deseq
interactions
multiple factor design
updated 8.3 years ago by
Michael Love
41k • written 8.3 years ago by
Stephen Turner
▴ 290
13
votes
20
replies
3.6k
views
cellCounts() function floating point error
Rsubread
24 months ago • updated 21 months ago
J-E
• 0
13
votes
16
replies
5.0k
views
Using edgeR or DESeq2 to analyze allele-specific expression?
edgeR
deseq2
ase
allele
8.6 years ago
trianglescout
▴ 40
13
votes
2
replies
6.4k
views
Using limma when continuous and categorical confounders are present at the same time (e.g.age, gender)
limma
covariate
continuous
categorical
adjustment
updated 8.8 years ago by
Gordon Smyth
50k • written 8.8 years ago by
sg45653
• 0
13
votes
11
replies
17k
views
edgeR TMM values
edger
8.3 years ago
ribioinfo
▴ 100
13
votes
21
replies
6.0k
views
modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
limma
voom
hurdle
single cell
8.7 years ago
osa.zuta
▴ 40
13
votes
3
replies
3.5k
views
EdgeR cpm: factor of 2 when adjusting library size?
edger
cpm
8.4 years ago
mikaelhc
▴ 20
13
votes
22
replies
27k
views
DESEq2 Paired samples Before and after treatment
deseq2
paired samples
updated 10 weeks ago by
Michael Love
41k • written 7.9 years ago by
adesrichard
▴ 30
13
votes
1
reply
4.6k
views
WGCNA - Compare module preservation between class
WGCNA
coexpression
updated 8.8 years ago by
Peter Langfelder
★ 3.0k • written 8.8 years ago by
abellonau
▴ 60
13
votes
2
replies
4.6k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA
goseq
topgo
gega
gostats
updated 8.5 years ago by
Robert Castelo
★ 3.3k • written 8.5 years ago by
jacorvar
▴ 40
13
votes
35
replies
16k
views
RDAVIDWebService Error 301: Moved Permanently
rdavidwebservice
david
updated 5.8 years ago by
gevermalc
• 0 • written 8.8 years ago by
Vivek.b
▴ 100
13
votes
8
replies
16k
views
how to use biomaRt with ensembl build 37
biomaRt
ensembl
GRCh37
updated 9.5 years ago by
Thomas Maurel
▴ 800 • written 9.6 years ago by
Pablo marin-garcia
▴ 90
13
votes
11
replies
12k
views
RNA-Seq, generate batch-free count matrix
edgeR
sva
updated 9.5 years ago by
Gordon Smyth
50k • written 9.8 years ago by
Brian Haas
▴ 90
13
votes
2
replies
3.1k
views
voom with combat
limma
voom
combat
batch effect
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
eldronzhou
▴ 10
13
votes
3
replies
2.1k
views
News:
Bioconductor teaching week
teaching
Carpentries
written 20 months ago by
Laurent Gatto
1.6k
12
votes
7
replies
4.1k
views
illumina ht-12 v4 expression beadchip
microarray
illumina human ht-12 v4
updated 7.2 years ago by
Gordon Smyth
50k • written 7.2 years ago by
arisarkar88
▴ 40
12
votes
15
replies
3.4k
views
error with HDF5Array
hdf5array
biocparallel
updated 6.0 years ago by
Mike Smith
★ 6.5k • written 6.0 years ago by
cath
▴ 30
12
votes
8
replies
1.9k
views
DESeq fitted values using coefficients vs mu
deseq2
updated 7.3 years ago by
Michael Love
41k • written 7.3 years ago by
Matthew McCall
▴ 830
12
votes
20
replies
2.0k
views
Possible implementation of multifactorial contrasts in limma regarding a microarray dataset
limma
multifactorial design
design and contrast matrix
affymetrix microarrays
updated 8.7 years ago by
Aaron Lun
★ 28k • written 8.7 years ago by
svlachavas
▴ 830
12
votes
3
replies
6.0k
views
Error while uploading Bioconductor packages - R Shiny
shiny
package
deploy
6.1 years ago
lloyd.izard
▴ 80
12
votes
4
replies
4.4k
views
differential expression analysis of htseq data with edgeR/voom
voom
htseq
edgeR
limma
RNASeq123
updated 5.3 years ago by
Gordon Smyth
50k • written 6.9 years ago by
wd
▴ 30
12
votes
33
replies
28k
views
Cannot install packages by BiocManager::install()
BiocManager
updated 2.0 years ago by
James W. MacDonald
65k • written 3.0 years ago by
mizzle
▴ 60
12
votes
10
replies
6.6k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva
gene set variation analysis
normalization
transformation
rna-seq
6.1 years ago • updated 5.3 years ago
rached
▴ 60
12
votes
10
replies
6.4k
views
edgeR glmLRT with test="F"?
edger
dge
differential expression
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
Ryan C. Thompson
★ 7.9k
12
votes
6
replies
1.6k
views
Testing for DE genes
affymetrix microarrays
limma
differential gene expression
updated 7.0 years ago by
Aaron Lun
★ 28k • written 7.0 years ago by
Lennart.Vermander
▴ 10
12
votes
9
replies
7.9k
views
Appropriate use of the function treat of the limma package
limma
treat
microarray
bioconductor
9.1 years ago
svlachavas
▴ 830
12
votes
6
replies
3.4k
views
Allele Specific Expression in DESeq2 or EdgeR
rnaseq
deseq2
edger
8.4 years ago
martiningi
▴ 40
12
votes
6
replies
12k
views
makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
software error
maketxdbfrombiomart
updated 8.4 years ago by
Maciej Jończyk
• 0 • written 8.5 years ago by
luigi.cerulo
▴ 40
12
votes
7
replies
1.9k
views
No method for coercing this S4 class to a vector, as trying to import my own data rather than using SRA in the workflow RnaSeqGeneEdgeRQL
rnaseqgeneedgerql
shortread
Rsubread
updated 5.1 years ago by
Aspie96
▴ 60 • written 5.1 years ago by
Raito92
▴ 60
12
votes
2
replies
3.5k
views
How does edgeR compare to lme4?
rna-seq
edger
mixed model
random effects
lme4
updated 7.9 years ago by
Gordon Smyth
50k • written 7.9 years ago by
Ekarl2
▴ 80
12
votes
6
replies
2.6k
views
How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
edger
differential gene expression
rnaseq
updated 7.1 years ago by
Gordon Smyth
50k • written 7.1 years ago by
gabriel.rosser
▴ 20
12
votes
12
replies
2.0k
views
FDR does not change between genes in edgeR
RNAseq
edgeR
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
apfelbapfel
▴ 30
1,000 results • Page
3 of 20
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
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swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
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I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
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This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
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