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6
votes
11
replies
975
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Packages don't update, but no error or warning is thrown
Bioconductor
3 months ago • updated 10 weeks ago
gernophil
• 0
6
votes
8
replies
1.2k
views
CAGEr bug report: wrong consensus cluster results
CAGEr
updated 9 months ago by
Charles Plessy
▴ 180 • written 17 months ago by
Meng
▴ 30
6
votes
5
replies
6.2k
views
Using Limma R package For Proteomics differential expression
limma
ProteomicsWorkflow
updated 7 months ago by
Gordon Smyth
50k • written 2.5 years ago by
David Lyon
▴ 340
6
votes
19
replies
2.4k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 13 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
6
votes
11
replies
26k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq
deseq2
updated 9 months ago by
Erika
• 0 • written 9.3 years ago by
c.lieftink@nki.nl
▴ 40
6
votes
6
replies
2.7k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna
WGCNA
written 4.0 years ago by
Colari19
▴ 60
6
votes
9
replies
751
views
biomaRt has encountered an unknown server error.
biomaRt
host
useEnsembl
updated 3 months ago by
alexander3
• 0 • written 3 months ago by
Amparo
• 0
6
votes
7
replies
942
views
[Bug] Segfault in edgeR::cpm
edgeR
segfault
updated 6 months ago by
ATpoint
★ 4.1k • written 6 months ago by
jonas.freimuth
▴ 20
5
votes
1
reply
434
views
News:
Bioconductor 3.18 is Released!
Packages
Bioconductor
Release
Software
written 6 months ago by
shepherl
3.8k
5
votes
5
replies
791
views
limma output for epic array methylation data
linearregression
epicarray
MethylationArray
limma
8 months ago
Jitendra
▴ 10
5
votes
6
replies
414
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 19 days ago by
ATpoint
★ 4.1k • written 22 days ago by
nhaus
▴ 30
5
votes
2
replies
685
views
PhD student
TMM
limma
10 months ago
Nisha
• 0
5
votes
5
replies
438
views
create COMPOUND dataset (2 matrices) with rhdf5?
rhdf5
3 months ago • updated 12 weeks ago
baptiste
▴ 20
5
votes
8
replies
1.5k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData
MicroarrayData
limma
updated 4 months ago by
Shaimaa Gamal
• 0 • written 11 months ago by
pg45863
▴ 10
5
votes
6
replies
644
views
DataFrame Construction With Non-standard Column
S4Vectors
updated 7 months ago by
Hervé Pagès
16k • written 7 months ago by
Dario Strbenac
★ 1.5k
5
votes
7
replies
1.1k
views
different number of DEG because of outliers
DESeq2
RNASeq
updated 3 months ago by
Gordon Smyth
50k • written 13 months ago by
Ilya
• 0
5
votes
3
replies
698
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom
blocking
limma
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
Gerhard Thallinger
▴ 180
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna
rnaseq
written 7.2 years ago by
panagiotis.mokos
▴ 40
5
votes
4
replies
387
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
10 weeks ago • updated 9 weeks ago
pl23
• 0
5
votes
7
replies
447
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 5 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Amit
• 0
5
votes
1
reply
1.4k
views
Support for new Illumina human methylation EPIC array v2
human
methylationArrayAnalysis
updated 3 months ago by
s.malik
• 0 • written 14 months ago by
jenniewoo
▴ 70
5
votes
9
replies
896
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
21 days ago • updated 14 days ago
Chris
• 0
5
votes
3
replies
702
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 5 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Jack S.
▴ 50
5
votes
4
replies
9.7k
views
Getting rs ids using chr coordinates | Biomart
SNP
rs id
Biomart
Chromosome
coordinates
updated 9 months ago by
James W. MacDonald
65k • written 3.7 years ago by
Mahan
• 0
5
votes
2
replies
547
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
annikagable
• 0
5
votes
6
replies
1.9k
views
Questions about using training sets and WGCNA module eigengenes generated separately for Pigengene package
Pigengene
5 months ago
kjngo
▴ 40
5
votes
2
replies
748
views
ComBat_seq function in sva package does not return a matrix
sva
ComBat
ComBat-seq
Bioconductor
ComBat_seq
7 months ago
Federico
▴ 10
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
mohammedtoufiq91
▴ 10
5
votes
25
replies
865
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 27 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Jitendra
▴ 10
5
votes
18
replies
7.5k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor
Install
DESeq2
updated 4 months ago by
picasa1983
• 0 • written 2.3 years ago by
Victor
• 0
5
votes
6
replies
3.8k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics
NPX
limma
updated 3 months ago by
briankleiboeker
• 0 • written 3.1 years ago by
r.i.s.alnuwaysir
▴ 10
5
votes
2
replies
677
views
outdated GEOmetadb.sqlite
GEOmetadb
14 months ago • updated 3 months ago
Robert Castelo
★ 3.3k
5
votes
2
replies
863
views
can't install DESeq2 ("unable to access index for repository")
biocmanager
DESeq2
8 months ago
Alessia
▴ 40
5
votes
11
replies
3.0k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 11 months ago by
Sabiha
▴ 20
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 9 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
5
votes
6
replies
542
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression
rnaseqGene
RNASeqData
3 months ago
Shaimaa Gamal
• 0
5
votes
9
replies
2.5k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger
calcnormfactors
updated 8 months ago by
Novice_cam
• 0 • written 6.4 years ago by
knaxerova
▴ 10
5
votes
19
replies
5.9k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 8 months ago by
liz.lamarca
• 0 • written 2.8 years ago by
kwangbom
▴ 10
5
votes
6
replies
845
views
ASpli checks fail on Linux due to missing dependency to statmod
ASpli
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
martin.grigorov
▴ 10
5
votes
15
replies
5.0k
views
Cross-species RNA-seq with DESeq2
deseq2
rnaseq
across species
updated 10 months ago by
James W. MacDonald
65k • written 6.8 years ago by
vtartaglio
▴ 10
5
votes
5
replies
1.9k
views
Archive location for Bioconductor packages
archive
updated 8 months ago by
shepherl
3.8k • written 20 months ago by
ems
▴ 20
5
votes
11
replies
4.2k
views
How to annotate gene names for genomic coordinates?
annotation
written 8.9 years ago by
seeker
• 0
5
votes
3
replies
2.0k
views
Cannot download GEOmetadb sqlite file
GEOmetadb
updated 12 weeks ago by
ilayahari
• 0 • written 6.5 years ago by
arnaud.ceol.pro
▴ 10
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 14 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
5
votes
7
replies
10.0k
views
threshold to filter lowly expressed genes
edger
rnaseq
updated 3 months ago by
Shaimaa Gamal
• 0 • written 7.1 years ago by
myprogramming2016
• 0
4
votes
7
replies
2.1k
views
should statmod be a dependency of limma and not a suggests?
limma
updated 9 months ago by
Gordon Smyth
50k • written 7.9 years ago by
nathan
• 0
4
votes
3
replies
1.8k
views
catchSalmon for tx-level DE
catchSalmon
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 3.5 years ago by
ATpoint
★ 4.1k
4
votes
2
replies
620
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
alvaroperona1
▴ 10
4
votes
16
replies
7.3k
views
Normalised counts from RUVg in RUVSeq
RUVg
ruvseq
rnaseq
updated 5 weeks ago by
Shaimaa Gamal
• 0 • written 9.0 years ago by
Pauly Lin
▴ 150
1,000 results • Page
2 of 20
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Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq
by
james.zhang20
• 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Answer: Deseq2 and Normalization of RNA sequencing data
by
ATpoint
★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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