0
votes
1
reply
17
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 2 hours ago by ★ 4.1k • written 2 hours ago by • 0
1
vote
2
replies
129
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
1 day ago • updated 8 hours ago Dylan.Sheerin • 0
0
votes
0
replies
16
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer ShinyApps
12 hours ago neilzhao ▴ 30
1
vote
0
replies
262
views
News: Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition Awards Bioconductor Bioc204
6 weeks ago • updated 20 hours ago shepherl 3.9k
0
votes
1
reply
44
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 1 day ago by ★ 4.1k • written 1 day ago by • 0
3
votes
4
replies
440
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 1 day ago by ★ 6.5k • written 4 days ago by • 0
2
votes
5
replies
151
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
2 days ago • updated 6 hours ago sajadahmad41454 • 0
0
votes
0
replies
27
views
Treeio as.treedata function seq lenght error
treeio
2 days ago nromerov • 0
1
vote
1
reply
109
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
updated 2 days ago by 65k • written 2 days ago by • 0
2
votes
9
replies
230
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
2 days ago • updated 11 hours ago Abbey • 0
1
vote
1
reply
96
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 2 days ago by 65k • written 3 days ago by • 0
0
votes
1
reply
61
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 2 days ago by 3.9k • written 2 days ago by • 0
0
votes
0
replies
44
views
need help with Diffbind multiple groups
DiffBind ChIPSeqData
3 days ago Dinesh • 0
3
votes
5
replies
207
views
Help with running egsea()
EGSEA
3 days ago • updated 2 days ago Chris • 0
3
votes
1
reply
102
views
How to save the DEXSeq results
DEXSeq
updated 3 days ago by 42k • written 3 days ago by • 0
3
votes
4
replies
221
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
updated 2 days ago by 50k • written 4 days ago by • 0
0
votes
3
replies
139
views
Couldn't connect to server while using "pathways"
graphite
updated 3 days ago by 42k • written 4 days ago by • 0
1
vote
1
reply
95
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 3 days ago by 42k • written 3 days ago by ▴ 70
1
vote
1
reply
137
views
Handling multiple differential expression comparisons
DESeq2
updated 4 days ago by 42k • written 6 days ago by ▴ 10
2
votes
2
replies
178
views
fgsea significant result
fgsea
5 days ago • updated 4 days ago Chris • 0
0
votes
39
replies
2.8k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
15 months ago • updated 18 hours ago Poonam • 0
0
votes
6
replies
242
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 6 days ago by ★ 1.4k • written 7 days ago by ▴ 130
1
vote
2
replies
355
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 6 days ago by 50k • written 6 days ago by • 0
2
votes
3
replies
197
views
package goseq seems to be not available on the latest version of R
goseq
updated 3 days ago by 50k • written 6 days ago by ▴ 20
2
votes
3
replies
203
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 5 days ago by ★ 4.1k • written 6 days ago by • 0
0
votes
0
replies
87
views
dba.plotProfile() plotting and interpretation
DiffBind
6 days ago Henry ▴ 10
0
votes
1
reply
138
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 7 days ago by 50k • written 7 days ago by • 0
0
votes
1
reply
123
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 7 days ago by 50k • written 7 days ago by • 0
4
votes
2
replies
571
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
7 days ago • updated 3 days ago gene_bioconductor ▴ 10
0
votes
0
replies
69
views
flowStats for CyTOF
flowStats
7 days ago tholmes • 0
0
votes
2
replies
125
views
DESeq2 v1.35.0
DESeq2
updated 7 days ago by 42k • written 7 days ago by • 0
0
votes
0
replies
61
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
7 days ago yvonneh • 0
0
votes
0
replies
58
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
7 days ago Ian D. ▴ 70
0
votes
1
reply
91
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 8 days ago by • 0
0
votes
3
replies
192
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
9 days ago • updated 2 days ago Ian D. ▴ 70
0
votes
2
replies
163
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
8 days ago • updated 7 days ago kcarey • 0
0
votes
3
replies
168
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 7 days ago by ★ 4.1k • written 8 days ago by • 0
1
vote
3
replies
257
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 2 days ago by ★ 4.1k • written 8 days ago by • 0
4
votes
0
replies
99
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
8 days ago shepherl 3.9k
0
votes
0
replies
113
views
Empty table plot using plotGseaTable()
fgsea
8 days ago • updated 6 days ago Chris • 0
0
votes
3
replies
182
views
Store output of matchPWM()
biostrings Biostrings
updated 8 days ago by 65k • written 8 days ago by ▴ 70
0
votes
3
replies
266
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 8 days ago by 42k • written 9 days ago by • 0
1
vote
2
replies
251
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
9 days ago • updated 8 days ago Yveto • 0
8
votes
7
replies
1.8k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 4 days ago by • 0 • written 6.7 years ago by ▴ 80
0
votes
1
reply
240
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 9 days ago by 65k • written 10 days ago by • 0
3
votes
4
replies
234
views
Help with error using camera() in limma
CAMERA limma
9 days ago Chris • 0
1
vote
1
reply
131
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 9 days ago by 42k • written 9 days ago by • 0
0
votes
2
replies
142
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
10 days ago • updated 7 days ago Aurora • 0
0
votes
1
reply
120
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 9 days ago by 42k • written 10 days ago by • 0
0
votes
0
replies
79
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
9 days ago Maria Doyle ▴ 70
1,000 results • Page 1 of 20
Recent ...
Replies
Answer: Differential gene expression analysis results by ATpoint ★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
Comment: deseq2 results by sajadahmad41454 • 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results by swbarnes2 ★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Dylan.Sheerin • 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Gordon Smyth 50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
Awards • All
Popular Question to Pietro ▴ 40
Popular Question to neilzhao ▴ 30
Popular Question to ATpoint ★ 4.1k
Teacher to Michael Love 42k
Popular Question to Haibo Liu • 0
Locations • All
Germany, 1 minute ago
Germany, 15 minutes ago
Italy, 17 minutes ago
Sweden, 28 minutes ago
France, 31 minutes ago
Traffic: 743 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