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9
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normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
51 minutes ago
piemmea
• 0
0
votes
1
reply
21
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
updated 1 hour ago by
Guido Hooiveld
★ 3.9k • written 2 hours ago by
Yveto
• 0
0
votes
42
replies
3.0k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 1 hour ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
0
votes
0
replies
16
views
DEXSeq design formula for multiple variable
DEXSeq
2 hours ago • updated 1 hour ago
Sara
• 0
0
votes
1
reply
47
views
ChAMP installation issue
Cha
ChAMP
updated 5 hours ago by
shepherl
3.9k • written 12 hours ago by
e1271094
• 0
0
votes
1
reply
59
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 8 hours ago by
Guido Hooiveld
★ 3.9k • written 1 day ago by
aogunbaw
• 0
2
votes
2
replies
233
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
6 days ago • updated 8 hours ago
zzrammal
• 0
0
votes
0
replies
21
views
Anti-Human APCS Recombinant Antibody (Dezamizumab)
healthyFlowData
13 hours ago
Lupe
• 0
0
votes
0
replies
39
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
1 day ago
Seungmin
• 0
0
votes
0
replies
46
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
1 day ago
Matthew Thornton
▴ 350
0
votes
4
replies
326
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 1 day ago by
Ziliang
• 0 • written 12 days ago by
Ian D.
▴ 70
0
votes
3
replies
7.8k
views
SingleR Label.Ont
SingleR
updated 2 days ago by
Denis
• 0 • written 8 months ago by
saeed.khalili
• 0
2
votes
7
replies
294
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
5 days ago • updated 2 days ago
sajadahmad41454
• 0
0
votes
0
replies
51
views
The 'Home' shows:An error has occurred. Check your logs or contact the app author for clarification.
Reports
2 days ago
315005358
• 0
1
vote
5
replies
501
views
Can't post a question containing code?
Bioconductor
updated 2 days ago by
NATASHA
• 0 • written 3 months ago by
DS
▴ 10
0
votes
1
reply
83
views
error
Biobase
2 days ago
NATASHA
• 0
3
votes
10
replies
383
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 3 days ago by
James W. MacDonald
65k • written 6 days ago by
Abbey
• 0
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 3 days ago by
maria.soler
• 0 • written 15 months ago by
kalavattam
▴ 10
0
votes
1
reply
84
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 3 days ago by
ATpoint
★ 4.1k • written 3 days ago by
sajadahmad41454
• 0
5
votes
3
replies
286
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 3 days ago by
Gordon Smyth
50k • written 25 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
192
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
4 days ago • updated 3 days ago
Dylan.Sheerin
• 0
0
votes
0
replies
40
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
3 days ago
neilzhao
▴ 30
0
votes
1
reply
1.3k
views
DSS CpG coverage threshold
DSS
WGBS
coverage
updated 4 days ago by
j.gilbert
• 0 • written 6.6 years ago by
floriandeckert
▴ 30
1
vote
0
replies
288
views
News:
Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition
Awards
Bioconductor
Bioc204
7 weeks ago • updated 4 days ago
shepherl
3.9k
0
votes
1
reply
73
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
sajadahmad41454
• 0
2
votes
4
replies
1.7k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
updated 4 days ago by
Chris
▴ 10 • written 7.4 years ago by
Pekka Kohonen
▴ 190
3
votes
4
replies
477
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 5 days ago by
Mike Smith
★ 6.5k • written 7 days ago by
robersy
• 0
1
vote
3
replies
278
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 5 days ago by
ATpoint
★ 4.1k • written 11 days ago by
angelathuynh5
• 0
1
vote
5
replies
1.5k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 5 days ago by
Jiayu
• 0 • written 5 months ago by
yanling
• 0
3
votes
5
replies
240
views
Help with running egsea()
EGSEA
6 days ago • updated 5 days ago
Chris
▴ 10
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 5 days ago by
Gordon Smyth
50k • written 5.6 years ago by
CantExitVIM
▴ 10
0
votes
0
replies
46
views
Treeio as.treedata function seq lenght error
treeio
5 days ago
nromerov
• 0
3
votes
4
replies
255
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
updated 5 days ago by
Gordon Smyth
50k • written 7 days ago by
Chris
▴ 10
4
votes
9
replies
463
views
Memory errors using read.bismark?
dmrseq
bsseq
4 weeks ago • updated 6 days ago
Juan Higareda
• 0
2
votes
1
reply
131
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
e1271094
• 0
0
votes
1
reply
82
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 6 days ago by
shepherl
3.9k • written 6 days ago by
cyril.dalmasso
• 0
0
votes
0
replies
64
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
6 days ago
Dinesh
• 0
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 6 days ago by
Caio
• 0 • written 13.1 years ago by
boczniak767
▴ 720
0
votes
3
replies
170
views
Couldn't connect to server while using "pathways"
graphite
updated 6 days ago by
Michael Love
42k • written 7 days ago by
fduguchunhui
• 0
4
votes
2
replies
596
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
10 days ago • updated 6 days ago
gene_bioconductor
▴ 10
3
votes
1
reply
120
views
How to save the DEXSeq results
DEXSeq
updated 7 days ago by
Michael Love
42k • written 7 days ago by
Sara
• 0
1
vote
1
reply
114
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 7 days ago by
Michael Love
42k • written 7 days ago by
mat149
▴ 70
1
vote
2
replies
199
views
Improving the design matrices vignette in RNAseq123
RNAseq123
21 days ago • updated 7 days ago
Lluís Revilla Sancho
▴ 730
2
votes
3
replies
221
views
package goseq seems to be not available on the latest version of R
goseq
updated 7 days ago by
Gordon Smyth
50k • written 9 days ago by
Patrycja
▴ 20
8
votes
7
replies
1.8k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 7 days ago by
Sara
• 0 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 7 days ago
Henrik Bengtsson
★ 2.4k
2
votes
2
replies
198
views
fgsea significant result
fgsea
8 days ago • updated 7 days ago
Chris
▴ 10
1
vote
1
reply
159
views
Handling multiple differential expression comparisons
DESeq2
updated 8 days ago by
Michael Love
42k • written 9 days ago by
Zainab
▴ 10
2
votes
3
replies
222
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 8 days ago by
ATpoint
★ 4.1k • written 9 days ago by
Reza
• 0
0
votes
6
replies
257
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 9 days ago by
swbarnes2
★ 1.4k • written 10 days ago by
arfranco
▴ 130
1,729 results • Page
1 of 35
Recent ...
Replies
Comment: Problem finding certain variables when importing a public database GSE73103
by
Guido Hooiveld
★ 3.9k
FWIW: when I would like to make use of publicly available data, I always use the website to explore which metadata is submitted to GEO (and…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
This is `blockLength=200000`, and providing `seg=seg`? It's alright that it's not identical. In the bootstrapped data, you will now have l…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Thank you, Michael. I used the script shared by you. The genomic distribution of the original and null loci looks like non-stationary. Plea…
Comment: ChAMP installation issue
by
shepherl
3.9k
Without showing the commands you tried and the full output including error it is impossible to help. Please provide additional information…
Answer: Gene set enrichment analysis
by
Guido Hooiveld
★ 3.9k
No, that is not possible. The idea of gene set enrichment analysis (GSEA) is that it checks which gene sets (pathways, GO categories) are e…
Votes
A: DEXSeq time course design
using variable in design formula
differential expression for Single-cell RNAseq data using edgeR
Why p value inconsistent when using different number of pathway score?
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
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