0
votes
1
reply
6
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 10 minutes ago by 42k • written 16 minutes ago by • 0
0
votes
2
replies
69
views
Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 2 hours ago by ▴ 10 • written 2 days ago by • 0
1
vote
0
replies
297
views
News: Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition Awards Bioconductor Bioc204
7 weeks ago • updated 3 hours ago shepherl 3.9k
0
votes
1
reply
20
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
updated 2 hours ago by 65k • written 3 hours ago by • 0
0
votes
1
reply
45
views
normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 3 hours ago by 42k • written 1 day ago by • 0
0
votes
1
reply
31
views
Retrieving ceRNA data from the starBase or ENCORI Web API
microRNA starBase ceRNA WebAPI ENCORI offtopic
updated 2 hours ago by 65k • written 7 hours ago by • 0
1
vote
0
replies
24
views
News: Ensembl 112 has been released.
ensembldb biomaRt ensemblrelease
9 hours ago Aleena ▴ 30
0
votes
0
replies
22
views
QSEA- Extraction of Normalized methylation across the samples
qsea ngsReports correlation
15 hours ago Researcher • 0
0
votes
5
replies
319
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 1 hour ago by 42k • written 1 day ago by • 0
0
votes
2
replies
78
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
21 hours ago • updated 4 hours ago Ashley • 0
3
votes
4
replies
235
views
Store output of matchPWM()
biostrings Biostrings
13 days ago • updated 21 hours ago mat149 ▴ 70
0
votes
1
reply
37
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
updated 3 hours ago by 42k • written 21 hours ago by ▴ 30
0
votes
2
replies
55
views
Problem finding certain variables when importing a public database GSE73103
GSEABase GenomicDistributionsData
1 day ago • updated 3 hours ago Yveto • 0
0
votes
0
replies
22
views
How to design DEXSeq formula for multiple variables
DEXSeq
1 day ago • updated 11 hours ago Sara • 0
0
votes
1
reply
71
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 1 day ago by ★ 3.9k • written 2 days ago by • 0
0
votes
3
replies
103
views
ChAMP installation issue
Cha ChAMP
1 day ago • updated 11 hours ago e1271094 • 0
0
votes
1
reply
196
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
2 days ago • updated 23 hours ago Matthew Thornton ▴ 350
0
votes
3
replies
8.0k
views
SingleR Label.Ont
SingleR
updated 3 days ago by • 0 • written 8 months ago by • 0
0
votes
1
reply
108
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 4 days ago by ★ 4.1k • written 4 days ago by • 0
1
vote
2
replies
208
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
5 days ago • updated 4 days ago Dylan.Sheerin • 0
0
votes
0
replies
45
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer ShinyApps
4 days ago neilzhao ▴ 30
0
votes
1
reply
82
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 5 days ago by ★ 4.1k • written 5 days ago by • 0
3
votes
4
replies
483
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 6 days ago by ★ 6.5k • written 8 days ago by • 0
2
votes
7
replies
324
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
6 days ago • updated 3 days ago sajadahmad41454 • 0
0
votes
0
replies
51
views
Treeio as.treedata function seq lenght error
treeio
6 days ago nromerov • 0
2
votes
2
replies
243
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
7 days ago • updated 1 day ago zzrammal • 0
3
votes
10
replies
405
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 4 days ago by 65k • written 7 days ago by • 0
2
votes
1
reply
136
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 7 days ago by 65k • written 7 days ago by • 0
0
votes
1
reply
85
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 7 days ago by 3.9k • written 7 days ago by • 0
0
votes
0
replies
69
views
need help with Diffbind multiple groups
DiffBind ChIPSeqData
7 days ago Dinesh • 0
3
votes
5
replies
251
views
Help with running egsea()
EGSEA
8 days ago • updated 6 days ago Chris ▴ 10
3
votes
1
reply
128
views
How to save the DEXSeq results
DEXSeq
updated 8 days ago by 42k • written 8 days ago by • 0
3
votes
4
replies
263
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
updated 6 days ago by 50k • written 8 days ago by ▴ 10
0
votes
3
replies
186
views
Couldn't connect to server while using "pathways"
graphite
updated 8 days ago by 42k • written 8 days ago by • 0
1
vote
1
reply
119
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 8 days ago by 42k • written 8 days ago by ▴ 70
1
vote
1
reply
166
views
Handling multiple differential expression comparisons
DESeq2
updated 9 days ago by 42k • written 11 days ago by ▴ 10
2
votes
2
replies
205
views
fgsea significant result
fgsea
9 days ago Chris ▴ 10
0
votes
44
replies
3.0k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
updated 8 hours ago by 42k • written 15 months ago by • 0
0
votes
6
replies
266
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 10 days ago by ★ 1.4k • written 11 days ago by ▴ 130
1
vote
2
replies
382
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 10 days ago by 50k • written 10 days ago by • 0
2
votes
3
replies
236
views
package goseq seems to be not available on the latest version of R
goseq
updated 8 days ago by 50k • written 10 days ago by ▴ 20
2
votes
3
replies
230
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 9 days ago by ★ 4.1k • written 11 days ago by • 0
0
votes
0
replies
107
views
dba.plotProfile() plotting and interpretation
DiffBind
11 days ago Henry ▴ 10
0
votes
1
reply
162
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 11 days ago by 50k • written 12 days ago by • 0
0
votes
1
reply
145
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 11 days ago by 50k • written 12 days ago by • 0
4
votes
2
replies
603
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
12 days ago • updated 8 days ago gene_bioconductor ▴ 10
0
votes
0
replies
89
views
flowStats for CyTOF
flowStats
12 days ago tholmes • 0
0
votes
2
replies
144
views
DESeq2 v1.35.0
DESeq2
updated 12 days ago by 42k • written 12 days ago by • 0
0
votes
0
replies
84
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
12 days ago yvonneh • 0
0
votes
0
replies
76
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
12 days ago Ian D. ▴ 70
1,000 results • Page 1 of 20
Recent ...
Replies
Answer: Assymetric MA plot with no overall trend by Michael Love 42k
> so many upregulated genes vs. downregulated, which I think is worrying Take a look at the plotCounts for a couple of the up-regulated …
Comment: Can I trust the differential expression analysis when the two groups overlap on by Michael Love 42k
I'm wondering about sample table mixup. How have you merged your sequencing data with the phenotype data (`colData`)?
Comment: Can I trust the differential expression analysis when the two groups overlap on by Eric Katagirya • 0
Thanks @mikelove , Using vst or rlog doesn't improve the segregation nor is there a remarkable difference when I use 1000 or 2000 most vari…
Answer: Batch effect correction: methylome data by zhouwanding ▴ 10
I agree that the batch variable should be better modeled as a co-variate than explicit batch correction. There is also RUVm (https://www.nc…
Comment: Can I trust the differential expression analysis when the two groups overlap on by Eric Katagirya • 0
Thanks @bioinfguru - I did the 3-D PCA plot ![PC1 vs PC3 plot][1] and also the scree plot ![Scree plot][2] but couldn't make much of the…
Votes
Ensembl 112 has been released.
A: Diffbind results - non uniform width
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Answer: Error EPICv2 ChAMP
Comment: Store output of matchPWM()
Awards • All
Popular Question to mat.lesche ▴ 90
Popular Question to jordi.planells • 0
Scholar to mat149 ▴ 70
Popular Question to Gordon Smyth 50k
Popular Question to maria.soler • 0
Locations • All
Denver, University of Colorado Anschutz Medical Campus, just now
United States, 1 minute ago
France, 5 minutes ago
UPF, Barcelona, Spain, 12 minutes ago
United States, 18 minutes ago
Traffic: 810 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6