1
vote
2
replies
284
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
11 days ago • updated 10 days ago Dylan.Sheerin • 0
0
votes
0
replies
87
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer ShinyApps
10 days ago neilzhao ▴ 30
0
votes
1
reply
114
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 11 days ago by ★ 4.1k • written 11 days ago by • 0
2
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7
replies
412
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
12 days ago • updated 9 days ago sajadahmad41454 • 0
0
votes
0
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77
views
Treeio as.treedata function seq lenght error
treeio
12 days ago nromerov • 0
2
votes
2
replies
286
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error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
13 days ago • updated 7 days ago zzrammal • 0
3
votes
10
replies
486
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 10 days ago by 65k • written 13 days ago by • 0
2
votes
1
reply
184
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 13 days ago by 65k • written 13 days ago by • 0
0
votes
1
reply
119
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 13 days ago by 3.9k • written 13 days ago by • 0
0
votes
0
replies
99
views
need help with Diffbind multiple groups
DiffBind ChIPSeqData
13 days ago Dinesh • 0
3
votes
5
replies
305
views
Help with running egsea()
EGSEA
13 days ago • updated 12 days ago Chris ▴ 10
3
votes
1
reply
153
views
How to save the DEXSeq results
DEXSeq
updated 14 days ago by 42k • written 14 days ago by • 0
4
votes
5
replies
337
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
14 days ago • updated 5 days ago Chris ▴ 10
0
votes
3
replies
234
views
Couldn't connect to server while using "pathways"
graphite
updated 13 days ago by 42k • written 14 days ago by • 0
2
votes
1
reply
148
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 14 days ago by 42k • written 14 days ago by ▴ 70
1
vote
1
reply
193
views
Handling multiple differential expression comparisons
DESeq2
updated 15 days ago by 42k • written 16 days ago by ▴ 10
2
votes
2
replies
233
views
fgsea significant result
fgsea
15 days ago • updated 14 days ago Chris ▴ 10
0
votes
44
replies
3.2k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
updated 6 days ago by 42k • written 15 months ago by • 0
0
votes
6
replies
305
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 16 days ago by ★ 1.4k • written 17 days ago by ▴ 130
1
vote
2
replies
409
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 16 days ago by 50k • written 16 days ago by • 0
2
votes
3
replies
279
views
package goseq seems to be not available on the latest version of R
goseq
updated 14 days ago by 50k • written 16 days ago by ▴ 20
2
votes
3
replies
258
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 15 days ago by ★ 4.1k • written 16 days ago by • 0
0
votes
0
replies
124
views
dba.plotProfile() plotting and interpretation
DiffBind
17 days ago Henry ▴ 10
0
votes
1
reply
180
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 17 days ago by 50k • written 17 days ago by • 0
0
votes
1
reply
163
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 17 days ago by 50k • written 17 days ago by • 0
4
votes
2
replies
634
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
17 days ago • updated 13 days ago gene_bioconductor ▴ 10
0
votes
0
replies
100
views
flowStats for CyTOF
flowStats
18 days ago tholmes • 0
0
votes
2
replies
174
views
DESeq2 v1.35.0
DESeq2
updated 18 days ago by 42k • written 18 days ago by • 0
0
votes
0
replies
95
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
18 days ago yvonneh • 0
0
votes
0
replies
88
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
18 days ago Ian D. ▴ 70
0
votes
1
reply
141
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 18 days ago by • 0
0
votes
4
replies
378
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 8 days ago by • 0 • written 19 days ago by ▴ 70
0
votes
2
replies
215
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
18 days ago • updated 17 days ago kcarey • 0
0
votes
3
replies
228
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 18 days ago by ★ 4.1k • written 18 days ago by • 0
1
vote
3
replies
306
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 12 days ago by ★ 4.1k • written 18 days ago by • 0
4
votes
0
replies
145
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
18 days ago shepherl 3.9k
0
votes
0
replies
142
views
Empty table plot using plotGseaTable()
fgsea
18 days ago • updated 16 days ago Chris ▴ 10
0
votes
3
replies
303
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 18 days ago by 42k • written 19 days ago by • 0
1
vote
2
replies
295
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
19 days ago • updated 18 days ago Yveto • 0
0
votes
1
reply
266
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 19 days ago by 65k • written 20 days ago by • 0
3
votes
4
replies
266
views
Help with error using camera() in limma
CAMERA limma
20 days ago • updated 19 days ago Chris ▴ 10
1
vote
1
reply
158
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 20 days ago by 42k • written 20 days ago by • 0
0
votes
2
replies
170
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
20 days ago • updated 17 days ago Aurora • 0
0
votes
1
reply
139
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 20 days ago by 42k • written 20 days ago by • 0
0
votes
0
replies
96
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
20 days ago Maria Doyle ▴ 70
0
votes
1
reply
124
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 20 days ago by 3.9k • written 20 days ago by • 0
0
votes
1
reply
138
views
putting my own expression data in deseq2
DESeq2
updated 20 days ago by ★ 4.1k • written 20 days ago by • 0
2
votes
2
replies
238
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
20 days ago Chris ▴ 10
0
votes
3
replies
282
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 20 days ago by 65k • written 21 days ago by • 0
0
votes
0
replies
96
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
21 days ago Chris ▴ 10
45,678 results • Page 2 of 914
Recent ...
Replies
Comment: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
We have some text about this particular question in the Frequently Asked Questions (FAQ) part of the software vignette.
Answer: How to run allelic imbalance in apeglm by Michael Love 42k
You can put 1 / 1 for the ratio when you are missing counts and then set the weight for that matrix cell to 1e-6. Let me know if that's …
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Got you. Thanks again for your comments.
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
Thanks so much for your comment. Yes, this makes sense to me, especially since the effect of the drug is subtle. But it raises a larger con…
Answer: ERROR; return code from pthread_create() is 22 by James W. MacDonald 65k
Seems OK to me. ``` > dat <- ReadAffy() > dat AffyBatch object size of arrays=744x744 features (20 kb) cdf=HG-U219 (49386 affyids) …
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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