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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 12 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
6
votes
9
replies
748
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
11
replies
969
views
Packages don't update, but no error or warning is thrown
Bioconductor
3 months ago • updated 10 weeks ago
gernophil
• 0
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
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
7
replies
938
views
[Bug] Segfault in edgeR::cpm
edgeR
segfault
updated 6 months ago by
ATpoint
★ 4.1k • written 6 months ago by
jonas.freimuth
▴ 20
6
votes
7
replies
559
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
aa.machado001
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 8 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
5
votes
1
reply
432
views
News:
Bioconductor 3.18 is Released!
Packages
Bioconductor
Release
Software
written 6 months ago by
shepherl
3.8k
5
votes
5
replies
789
views
limma output for epic array methylation data
linearregression
epicarray
MethylationArray
limma
8 months ago
Jitendra
▴ 10
5
votes
5
replies
436
views
create COMPOUND dataset (2 matrices) with rhdf5?
rhdf5
3 months ago • updated 12 weeks ago
baptiste
▴ 20
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 13 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
5
votes
6
replies
411
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 18 days ago by
ATpoint
★ 4.1k • written 22 days ago by
nhaus
▴ 30
5
votes
2
replies
683
views
PhD student
TMM
limma
10 months ago
Nisha
• 0
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
643
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
697
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
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
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
383
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
10 weeks ago • updated 9 weeks ago
pl23
• 0
5
votes
7
replies
444
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 5 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Amit
• 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
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
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
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
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
3
replies
701
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 4 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Jack S.
▴ 50
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
2
replies
546
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
538
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression
rnaseqGene
RNASeqData
3 months ago
Shaimaa Gamal
• 0
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
843
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
25
replies
856
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 26 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Jitendra
▴ 10
5
votes
2
replies
746
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
11
replies
4.2k
views
How to annotate gene names for genomic coordinates?
annotation
written 8.9 years ago by
seeker
• 0
5
votes
9
replies
894
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
21 days ago • updated 13 days ago
Chris
• 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
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
5
votes
2
replies
674
views
outdated GEOmetadb.sqlite
GEOmetadb
14 months ago • updated 3 months ago
Robert Castelo
★ 3.3k
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
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
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
11
replies
3.0k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 11 months ago by
Sabiha
▴ 20
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
615
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: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM()
by
James W. MacDonald
65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Comment: DEseq2 coefficient
by
JKim
• 0
Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…
Votes
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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