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0
votes
2
replies
1.1k
views
p-values histogram in case of no effect
deseq2
10.7 years ago
itamarkanter
• 0
3
votes
5
replies
2.0k
views
weird model design for DE analysis
RNASeq
updated 5 months ago by
Gordon Smyth
53k • written 12.5 years ago by
Lorena Pantano
▴ 140
21
votes
5
replies
19k
views
using duplicateCorrelation with limma+voom for RNA-seq data
limma
voom
updated 10.7 years ago by
Gordon Smyth
53k • written 11.7 years ago by
John Blischak
▴ 190
2
votes
5
replies
6.3k
views
Can I use the WGCNA dendrogram to display a heatmap of gene expression?
wgcna
heatmap
desq2
clustering
updated 10.7 years ago by
Dario Strbenac
★ 1.6k • written 10.7 years ago by
Jon Bråte
▴ 270
0
votes
2
replies
2.3k
views
pdInfoBuilder fails on Affy's GeneChip Human Transcriptome Array 2.0
BiocViews
Annotation
Organism
biocViews
oligo
oligoClasses
BiocViews
BiocViews
Annotation
updated 10.7 years ago by
Jason Hubbard
▴ 20 • written 12.0 years ago by
Guilherme Rocha
▴ 40
1
vote
2
replies
3.9k
views
Affy HTA 2.0 array analysis
Annotation
affy
Annotation
affy
updated 10.7 years ago by
Jason Hubbard
▴ 20 • written 12.4 years ago by
He, Yiwen NIH/CIT
▴ 360
1
vote
2
replies
1.9k
views
Question about read.maimages
differential gene expression
limma
read.maimages
updated 10.7 years ago by
Gordon Smyth
53k • written 10.7 years ago by
SSK
▴ 10
6
votes
3
replies
3.7k
views
vooma lm.fit versus voom lmFit
limma
updated 10.7 years ago by
Gordon Smyth
53k • written 10.7 years ago by
biominer
▴ 10
12
votes
7
replies
23k
views
DESEq2 comparison with mulitple cell types under 2 conditions
deseq2
multiple factor design
updated 8 months ago by
boczniak767
▴ 740 • written 10.7 years ago by
kmu004
▴ 50
1
vote
4
replies
2.2k
views
"BiocGenerics:::testPackage('PackageName')" works from R console but fails using "R CMD check PackageName" at terminal
software error
cmd check
bioconductor
10.7 years ago
Wade Copeland
▴ 20
0
votes
1
reply
1.8k
views
workflowInstall issues; missing Windows binary
software error
missing data
workflowinstall
10.7 years ago
anoll2
• 0
0
votes
2
replies
3.8k
views
Using RNA-Seq Workflow using Real Life FASTQ data - and Mouse Reference Genome
deseq2
deseqdataset
rnaseqgene
fastq
reference genome
updated 10.7 years ago by
James W. MacDonald
68k • written 10.7 years ago by
greg.mulhearn
• 0
0
votes
31
replies
6.3k
views
Error in find DEXSeq package
deseq
dexseq
10.7 years ago
engr.yahya602
• 0
0
votes
0
replies
1.9k
views
Circos Styling plots is now easy with canceR package
canceR
visualization
omiccircos
10.7 years ago
kmezhoud
▴ 10
3
votes
16
replies
22k
views
featureCounts - paired-end data
featurecounts
rsubread
updated 2.6 years ago by
Robert
• 0 • written 10.7 years ago by
samuel collombet
▴ 140
3
votes
2
replies
3.2k
views
Normalisation before RUVg and RUV2?
ruvseq
ruv
updated 10.7 years ago by
davide risso
▴ 980 • written 10.7 years ago by
Pauly Lin
▴ 160
0
votes
0
replies
1.3k
views
Creating model for DE analysis in tweeDEglm
tweedeseq
10.7 years ago
keever1
• 0
1
vote
1
reply
2.1k
views
Error in Package GEOquery
geoquery
error
R
microarray
updated 10.7 years ago by
James W. MacDonald
68k • written 10.7 years ago by
pankajnarula84
▴ 20
2
votes
2
replies
4.1k
views
How to Normalize the Microarray Data Obtained from ncbi?
microarray
normalization
ncbi
updated 10.7 years ago by
James W. MacDonald
68k • written 10.7 years ago by
pankajnarula84
▴ 20
1
vote
6
replies
4.5k
views
Calculate DESeq2 fold change of 1 gene to 1 of the sample
deseq2
updated 10.7 years ago by
Simon Anders
★ 3.8k • written 10.7 years ago by
bharata1803
▴ 60
0
votes
1
reply
2.2k
views
Using PCA for unsupervised clustering of RNA-Seq with DESeq2
rnaseq
pca
deseq2
clustering
updated 10.7 years ago by
Michael Love
43k • written 10.7 years ago by
Nick N
▴ 60
1
vote
3
replies
3.6k
views
DESeq2 effects of treatment at different time points including subject ID
deseq2
rnaseq
differential gene expression
10.7 years ago
Catalina Aguilar Hurtado
▴ 90
0
votes
1
reply
1.0k
views
Problems facing package installation
software error
updated 10.7 years ago by
Martin Morgan
25k • written 10.7 years ago by
moinulhq07
• 0
0
votes
0
replies
1.1k
views
clearing variables in SELEX package
SELEX
10.7 years ago
sarifkin
• 0
0
votes
3
replies
1.8k
views
Differential Expression of c.diff. microarray
arrayexpress
differential expression
10.7 years ago
SSK
▴ 10
5
votes
12
replies
3.0k
views
DESeq2 multi-factor comparison problem
deseq2
rnaseq
10.7 years ago
Vivek.b
▴ 100
3
votes
5
replies
15k
views
cannot find -llapack + -lblas for package install
lblas
llapack
LinuxMint
10.7 years ago
Eric P
▴ 10
2
votes
3
replies
3.8k
views
Diffbind counts vs. MACS2 scores
diffbind
10.7 years ago
mm2489
▴ 20
0
votes
6
replies
2.7k
views
is it possible to find sample batch # in CEL files?
PROcess
PROcess
updated 10.7 years ago by
suprun.maria
• 0 • written 13.0 years ago by
Brian Tsai
▴ 40
3
votes
9
replies
2.9k
views
retreiving peak caller fold enrichments after generating consensus peakset in DiffBind
diffbind
updated 10.7 years ago by
Rory Stark
★ 5.2k • written 10.7 years ago by
mm2489
▴ 20
0
votes
0
replies
1.3k
views
crlmm: RFC - new feature to work on subsets of CEL files
crlmm
10.7 years ago
Karl Forner
▴ 70
3
votes
5
replies
3.9k
views
PlotMA Error_Coercing to a vector
deseq2
10.7 years ago
Jessica Chen
▴ 20
3
votes
6
replies
4.4k
views
Check understanding of linear model
linear model
deseq2
updated 10.7 years ago by
James W. MacDonald
68k • written 10.7 years ago by
Jake
▴ 90
0
votes
4
replies
2.1k
views
gcContent error with shortread
shortread
10.7 years ago
danova_fr
▴ 20
2
votes
20
replies
12k
views
problem loading lumi package, Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'
lumi
updated 10.7 years ago by
laseaman
• 0 • written 11.2 years ago by
lucashusquin
▴ 10
2
votes
0
replies
2.4k
views
Job:
23andMe Job Opportunities
bioinformatician job
bioinformatics scientist
genetics
Job
10.7 years ago
rgentleman
★ 5.5k
7
votes
3
replies
1.7k
views
Extracting first member of each element of a matrix of lists
variantannotation
vcf
updated 10.7 years ago by
Michael Lawrence
★ 11k • written 10.7 years ago by
Sean Davis
21k
1
vote
8
replies
4.5k
views
Intepretation of RUVseq/edgeR logFC
RUVseq
logFC
edgeR
10.7 years ago
Marie
• 0
0
votes
7
replies
2.3k
views
DiffBind fails to derive consensus peaksets
software error
chipseq
diffbind
updated 10.7 years ago by
Gord Brown
▴ 670 • written 10.7 years ago by
Nicolas Delhomme
▴ 320
0
votes
1
reply
2.5k
views
Scaled venn/euler diagram using makeVennDiagram
ChIPpeakAnno
venn diagram
updated 10.7 years ago by
Ou, Jianhong
★ 1.3k • written 10.7 years ago by
da.de
▴ 30
2
votes
2
replies
6.7k
views
What are logCPM values in the Differentially Expressed Genes output
edgeR
10.7 years ago
candida.vaz
▴ 50
1
vote
9
replies
3.9k
views
RUV: removing unwanted variation in RNA-seq
RUV
ruvseq
rnaseq
10.7 years ago
sergio.espeso-gil
• 0
1
vote
4
replies
1.7k
views
Specifically expressed genes
DESeq2
specific expression
rnaseq
clustering
differential expression
updated 10.7 years ago by
Michael Love
43k • written 10.7 years ago by
arrigonialberto86
• 0
0
votes
0
replies
1.5k
views
Unexpected recursive unlist of bplapply (BiocParallel) results when using only one worker
biocparallel
bplapply
10.7 years ago
akaever
▴ 30
0
votes
5
replies
2.7k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq
RRBS
SAAP-BS
coverage
10.7 years ago
maria.maqueda
• 0
0
votes
0
replies
1.2k
views
RamiGO: getAmigoTree producing internal server errors
ramigo
10.7 years ago
Asta Laiho
▴ 120
1
vote
0
replies
2.4k
views
Job:
Postdoctoral Research Fellow in Bioinformatics - Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Mainz, Germany
bioinformatician job
rnaseq
statistics
systemsbiology
Job
10.7 years ago
Federico Marini
▴ 180
4
votes
2
replies
4.3k
views
Cannot load or update GO.db
GO.db
bioclite
10.7 years ago
Steve Pederson
▴ 170
9
votes
2
replies
6.1k
views
Limma Model Matrix Understanding
limma
limma design matrix
model matrix
updated 10.7 years ago by
Aaron Lun
★ 29k • written 10.7 years ago by
andrew.j.skelton73
▴ 370
1
vote
2
replies
2.8k
views
readCufflinks omits gene name, ID replaced with XLOC_ ID. Any way to correct this?
cummerbund
updated 10.7 years ago by
andrew.j.skelton73
▴ 370 • written 10.7 years ago by
daniel.antony.pass
• 0
46,726 results • Page
458 of 935
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Martin Morgan
25k
I see rstudioapi in the `sessionInfo()`. RStudio does not support forked ('multicore') processes. Does the BiocParallel example work when y…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
Given that this is an issue with BiocParallel on your machine and we have a minimal reproducible example, you may want to repost the issue.…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
ATpoint
★ 5.0k
Yes, still it's not reproducible, yet hard to debug. I cannot reproduce myself either.
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Benjamin
• 0
Still happening using pre-existing size factors estimating dispersions gene-wise dispersion estimates: 15 workers mean-dis…
Answer: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Benjamin
• 0
Still happening in a clean install
Votes
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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