2
votes
2
replies
285
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
12 days ago • updated 7 days ago zzrammal • 0
3
votes
10
replies
483
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 10 days ago by 65k • written 12 days ago by • 0
0
votes
1
reply
118
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 13 days ago by 3.9k • written 13 days ago by • 0
2
votes
1
reply
182
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 13 days ago by 65k • 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
304
views
Help with running egsea()
EGSEA
13 days ago • updated 12 days ago Chris ▴ 10
3
votes
1
reply
151
views
How to save the DEXSeq results
DEXSeq
updated 14 days ago by 42k • written 14 days ago by • 0
2
votes
1
reply
147
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 14 days ago by 42k • written 14 days ago by ▴ 70
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
4
votes
5
replies
335
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
14 days ago • updated 5 days ago Chris ▴ 10
7
votes
6
replies
613
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
written 14 days ago by • 0
2
votes
2
replies
232
views
fgsea significant result
fgsea
15 days ago • updated 14 days ago Chris ▴ 10
1
vote
2
replies
407
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
277
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
1
vote
1
reply
193
views
Handling multiple differential expression comparisons
DESeq2
updated 15 days ago by 42k • written 16 days ago by ▴ 10
0
votes
0
replies
124
views
dba.plotProfile() plotting and interpretation
DiffBind
16 days ago Henry ▴ 10
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
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
1
reply
179
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
0
votes
0
replies
99
views
flowStats for CyTOF
flowStats
17 days ago tholmes • 0
0
votes
2
replies
172
views
DESeq2 v1.35.0
DESeq2
updated 17 days ago by 42k • written 17 days ago by • 0
0
votes
0
replies
93
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
17 days ago yvonneh • 0
0
votes
0
replies
88
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
17 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
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
144
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
18 days ago shepherl 3.9k
0
votes
0
replies
140
views
Empty table plot using plotGseaTable()
fgsea
18 days ago • updated 16 days ago Chris ▴ 10
3
votes
4
replies
292
views
Store output of matchPWM()
biostrings Biostrings
18 days ago • updated 6 days ago mat149 ▴ 70
0
votes
4
replies
377
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 8 days ago by • 0 • written 19 days ago by ▴ 70
1
vote
2
replies
294
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
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
3
votes
4
replies
266
views
Help with error using camera() in limma
CAMERA limma
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
0
replies
96
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
20 days ago Maria Doyle ▴ 70
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
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
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
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
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
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
0
replies
96
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
21 days ago • updated 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 19 days ago by 65k • written 21 days ago by • 0
3
votes
3
replies
271
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 21 days ago by ★ 4.1k • written 21 days ago by ▴ 10
1
vote
1
reply
154
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 23 days ago by ▴ 40 • written 24 days ago by ★ 1.5k
1
vote
3
replies
255
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 24 days ago by 42k • written 24 days ago by • 0
1
vote
7
replies
361
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
24 days ago • updated 23 days ago pl23 • 0
45,678 results • Page 2 of 914
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Answer: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 65k
Unless you think the different lines or tissues will have very different within-group variances, you should just analyze together and make …
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments? by James W. MacDonald 65k
It appears that batch is orthogonal to the treatment, so you can just fit a batch effect in your model.
Answer: Control group between 2 batches have different expression in RNAseq data by James W. MacDonald 65k
Since batch is orthogonal to the treatment, you just add a batch factor to your model.
Answer: Subsetting RNAseq data | voomaByGroup() by Anna • 0
Hi Gordon. Thank you so much. Your reply is extremely helpful, and I feel more confident moving forward with the analysis. Also, very inte…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
edgeR used a prior count which stabilizes LFC while DESeq2 does not. Note that the SE are larger in these cases so you don't have experime…
Votes
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
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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