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6
votes
6
replies
2.8k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna
WGCNA
written 4.1 years ago by
Colari19
▴ 60
6
votes
11
replies
4.0k
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 9 weeks ago by
Priya
• 0 • written 3.2 years ago by
Marina
▴ 40
6
votes
5
replies
6.2k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0
minfi
updated 6 months ago by
jay
▴ 10 • written 14 months ago by
luca.s
▴ 50
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
11
replies
1.1k
views
Packages don't update, but no error or warning is thrown
Bioconductor
3 months ago
gernophil
• 0
6
votes
5
replies
1.2k
views
error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark.
bsseq
updated 8 months ago by
Peter Hickey
▴ 740 • written 9 months ago by
richardallenfriedmanbrooklyn
▴ 20
6
votes
9
replies
868
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
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 4 weeks ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
6
votes
12
replies
5.1k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 28 days ago
shepherl
3.9k
6
votes
2
replies
748
views
How to access the C++ code of the function .cxx_ave_log_cpm in the aveLogCPM.default function of EdgeR package?
edgeR
10 months ago
Josué
▴ 20
5
votes
2
replies
803
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
1
reply
465
views
News:
Bioconductor 3.18 is Released!
Packages
Bioconductor
Release
Software
written 6 months ago by
shepherl
3.9k
5
votes
5
replies
478
views
create COMPOUND dataset (2 matrices) with rhdf5?
rhdf5
3 months ago
baptiste
▴ 20
5
votes
3
replies
742
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 7 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
Jack S.
▴ 50
5
votes
5
replies
2.0k
views
Archive location for Bioconductor packages
archive
updated 9 months ago by
shepherl
3.9k • written 21 months ago by
ems
▴ 20
5
votes
5
replies
827
views
limma output for epic array methylation data
linearregression
epicarray
MethylationArray
limma
9 months ago
Jitendra
▴ 10
5
votes
7
replies
10k
views
threshold to filter lowly expressed genes
edger
rnaseq
updated 4 months ago by
Shaimaa Gamal
• 0 • written 7.2 years ago by
myprogramming2016
• 0
5
votes
6
replies
672
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
2
replies
695
views
outdated GEOmetadb.sqlite
GEOmetadb
15 months ago • updated 3 months ago
Robert Castelo
★ 3.3k
5
votes
7
replies
493
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 7 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
Amit
• 0
5
votes
8
replies
4.0k
views
Problem about picking soft threshold power in WGCNA software
wgcna
rnaseq
written 7.2 years ago by
panagiotis.mokos
▴ 40
5
votes
3
replies
2.0k
views
Cannot download GEOmetadb sqlite file
GEOmetadb
updated 3 months ago by
ilayahari
• 0 • written 6.5 years ago by
arnaud.ceol.pro
▴ 10
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
7
replies
1.1k
views
different number of DEG because of outliers
DESeq2
RNASeq
updated 4 months ago by
Gordon Smyth
50k • written 14 months ago by
Ilya
• 0
5
votes
3
replies
723
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom
blocking
limma
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
Gerhard Thallinger
▴ 180
5
votes
4
replies
9.8k
views
Getting rs ids using chr coordinates | Biomart
SNP
rs id
Biomart
Chromosome
coordinates
updated 10 months ago by
James W. MacDonald
65k • written 3.8 years ago by
Mahan
• 0
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 18 days ago by
James W. MacDonald
65k • written 2.4 years ago by
yanchangjian2019
• 0
5
votes
6
replies
1.9k
views
Questions about using training sets and WGCNA module eigengenes generated separately for Pigengene package
Pigengene
6 months ago
kjngo
▴ 40
5
votes
4
replies
434
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
3 months ago • updated 12 weeks ago
pl23
• 0
5
votes
25
replies
993
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Jitendra
▴ 10
5
votes
15
replies
5.1k
views
Cross-species RNA-seq with DESeq2
deseq2
rnaseq
across species
updated 11 months ago by
James W. MacDonald
65k • written 6.9 years ago by
vtartaglio
▴ 10
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 9 months ago by
Novice_cam
• 0 • written 6.5 years ago by
knaxerova
▴ 10
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 4 weeks ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
5
votes
18
replies
7.6k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor
Install
DESeq2
updated 5 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 3.2 years ago by
r.i.s.alnuwaysir
▴ 10
5
votes
11
replies
3.2k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 11 months ago by
Sabiha
▴ 20
5
votes
8
replies
8.9k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 27 days ago by
hortense96
• 0 • written 7.8 years ago by
dmcleanuk
▴ 30
5
votes
6
replies
886
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
2
replies
919
views
can't install DESeq2 ("unable to access index for repository")
biocmanager
DESeq2
9 months ago
Alessia
▴ 40
5
votes
8
replies
1.5k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData
MicroarrayData
limma
updated 5 months ago by
Shaimaa Gamal
• 0 • written 12 months ago by
pg45863
▴ 10
5
votes
6
replies
462
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 5 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
nhaus
▴ 30
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 12 months ago by
mohammedtoufiq91
▴ 10
5
votes
2
replies
703
views
PhD student
TMM
limma
10 months ago
Nisha
• 0
5
votes
9
replies
980
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 4 weeks ago
Chris
▴ 10
5
votes
3
replies
318
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 10 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Shaimaa Gamal
• 0
5
votes
19
replies
6.0k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 9 months ago by
liz.lamarca
• 0 • written 2.8 years ago by
kwangbom
▴ 10
5
votes
6
replies
609
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression
rnaseqGene
RNASeqData
4 months ago • updated 3 months ago
Shaimaa Gamal
• 0
5
votes
1
reply
1.4k
views
Support for new Illumina human methylation EPIC array v2
human
methylationArrayAnalysis
updated 4 months ago by
s.malik
• 0 • written 14 months ago by
jenniewoo
▴ 70
5
votes
2
replies
607
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 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 8.0 years ago by
nathan
• 0
1,742 results • Page
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Comment: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
We have some text about this particular question in the Frequently Asked Questions (FAQ) part of the software vignette.
Answer: How to run allelic imbalance in apeglm
by
Michael Love
42k
You can put 1 / 1 for the ratio when you are missing counts and then set the weight for that matrix cell to 1e-6. Let me know if that's …
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Got you. Thanks again for your comments.
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
Thanks so much for your comment. Yes, this makes sense to me, especially since the effect of the drug is subtle. But it raises a larger con…
Answer: ERROR; return code from pthread_create() is 22
by
James W. MacDonald
65k
Seems OK to me. ``` > dat <- ReadAffy() > dat AffyBatch object size of arrays=744x744 features (20 kb) cdf=HG-U219 (49386 affyids) …
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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