3
votes
4
replies
303
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 10 hours ago by ★ 6.5k • written 3 days ago by • 0
0
votes
2
replies
56
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
updated 5 hours ago by ★ 1.3k • written 14 hours ago by • 0
0
votes
0
replies
18
views
Treeio as.treedata function seq lenght error
treeio
19 hours ago nromerov • 0
1
vote
1
reply
83
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
updated 1 day ago by 65k • written 1 day ago by • 0
1
vote
6
replies
144
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 13 hours ago by ★ 3.3k • written 1 day ago by • 0
1
vote
1
reply
78
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 1 day ago by 65k • written 1 day ago by • 0
0
votes
1
reply
47
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 1 day ago by 3.9k • written 1 day ago by • 0
0
votes
0
replies
31
views
need help with Diffbind multiple groups
DiffBind ChIPSeqData
2 days ago Dinesh • 0
3
votes
5
replies
184
views
Help with running egsea()
EGSEA
2 days ago • updated 18 hours ago Chris • 0
1
vote
0
replies
235
views
News: Nominations for Bioconductor Awards 2024!
Recognition Awards Bioconductor Bioc204
6 weeks ago • updated 2 days ago shepherl 3.9k
3
votes
1
reply
87
views
How to save the DEXSeq results
DEXSeq
updated 2 days ago by 42k • written 2 days ago by • 0
3
votes
4
replies
207
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
updated 23 hours ago by 50k • written 2 days ago by • 0
0
votes
3
replies
120
views
Couldn't connect to server while using "pathways"
graphite
updated 2 days ago by 42k • written 2 days ago by • 0
1
vote
1
reply
84
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 2 days ago by 42k • written 2 days ago by ▴ 70
1
vote
1
reply
125
views
Handling multiple differential expression comparisons
DESeq2
updated 3 days ago by 42k • written 5 days ago by ▴ 10
2
votes
2
replies
158
views
fgsea significant result
fgsea
3 days ago Chris • 0
0
votes
35
replies
2.6k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
updated 3 hours ago by 42k • written 15 months ago by • 0
0
votes
6
replies
229
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 4 days ago by ★ 1.3k • written 6 days ago by ▴ 130
1
vote
2
replies
343
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 4 days ago by 50k • written 5 days ago by • 0
2
votes
3
replies
177
views
package goseq seems to be not available on the latest version of R
goseq
updated 2 days ago by 50k • written 5 days ago by ▴ 20
2
votes
3
replies
188
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 3 days ago by ★ 4.1k • written 5 days ago by • 0
0
votes
0
replies
75
views
dba.plotProfile() plotting and interpretation
DiffBind
5 days ago Henry ▴ 10
0
votes
1
reply
132
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 5 days ago by 50k • written 6 days ago by • 0
0
votes
1
reply
111
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 5 days ago by 50k • written 6 days ago by • 0
4
votes
2
replies
550
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
6 days ago • updated 2 days ago gene_bioconductor ▴ 10
0
votes
0
replies
60
views
flowStats for CyTOF
flowStats
6 days ago tholmes • 0
0
votes
2
replies
116
views
DESeq2 v1.35.0
DESeq2
updated 6 days ago by 42k • written 6 days ago by • 0
0
votes
0
replies
54
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
6 days ago yvonneh • 0
0
votes
0
replies
50
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
6 days ago Ian D. ▴ 70
0
votes
1
reply
81
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 6 days ago by • 0
0
votes
3
replies
171
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
7 days ago • updated 12 hours ago Ian D. ▴ 70
0
votes
2
replies
153
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
6 days ago • updated 5 days ago kcarey • 0
0
votes
3
replies
157
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 6 days ago by ★ 4.1k • written 6 days ago by • 0
1
vote
3
replies
240
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 14 hours ago by ★ 4.1k • written 7 days ago by • 0
3
votes
0
replies
91
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
7 days ago shepherl 3.9k
0
votes
0
replies
97
views
Empty table plot using plotGseaTable()
fgsea
7 days ago • updated 5 days ago Chris • 0
0
votes
3
replies
168
views
Store output of matchPWM()
biostrings Biostrings
updated 7 days ago by 65k • written 7 days ago by ▴ 70
0
votes
3
replies
261
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 7 days ago by 42k • written 7 days ago by • 0
1
vote
2
replies
242
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
7 days ago • updated 6 days ago Yveto • 0
8
votes
7
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 2 days ago by • 0 • written 6.7 years ago by ▴ 80
0
votes
1
reply
235
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 8 days ago by 65k • written 8 days ago by • 0
3
votes
4
replies
225
views
Help with error using camera() in limma
CAMERA limma
8 days ago Chris • 0
1
vote
1
reply
123
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 8 days ago by 42k • written 8 days ago by • 0
0
votes
2
replies
132
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
8 days ago • updated 5 days ago Aurora • 0
0
votes
1
reply
112
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 8 days ago by 42k • written 9 days ago by • 0
0
votes
0
replies
73
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
8 days ago Maria Doyle ▴ 70
0
votes
1
reply
98
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 8 days ago by 3.9k • written 8 days ago by • 0
0
votes
1
reply
115
views
putting my own expression data in deseq2
DESeq2
updated 8 days ago by ★ 4.1k • written 8 days ago by • 0
2
votes
2
replies
207
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
9 days ago Chris • 0
0
votes
3
replies
248
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 8 days ago by 65k • written 9 days ago by • 0
45,630 results • Page 1 of 913
Recent ...
Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results by swbarnes2 ★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
Awards • All
Teacher to Michael Love 42k
Popular Question to Haibo Liu • 0
Popular Question to HS ▴ 10
Popular Question to DevelopingHippo • 0
Scholar to Robert Castelo ★ 3.3k
Locations • All
WEHI, Melbourne, Australia, 17 minutes ago
Seattle, WA, United States, 1 hour ago
Mexico, 1 hour ago
Colombia, 2 hours ago
United States, 2 hours ago
Traffic: 612 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