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2
votes
2
replies
198
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
25 days ago
julia_mcdonough
• 0
2
votes
5
replies
245
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 12 days ago by
James W. MacDonald
65k • written 14 days ago by
bandconductor
• 0
2
votes
13
replies
431
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
16 days ago • updated 13 days ago
fernanda.backsouza
▴ 10
2
votes
2
replies
141
views
fgsea significant result
fgsea
3 days ago • updated 2 days ago
Chris
• 0
1
vote
4
replies
210
views
minfi::read.metharray.exp
minfiData
minfi
updated 13 days ago by
Basti
▴ 780 • written 15 days ago by
clacarion
• 0
1
vote
2
replies
161
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
13 days ago • updated 12 days ago
ATpoint
★ 4.1k
1
vote
1
reply
116
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 7 days ago by
Michael Love
42k • written 7 days ago by
marcusn
• 0
1
vote
3
replies
227
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 11 days ago by
Michael Love
42k • written 12 days ago by
JalapenoCornbread
• 0
1
vote
3
replies
229
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
Hervé Pagès
16k • written 2 days ago by
robersy
• 0
1
vote
1
reply
107
views
Handling multiple differential expression comparisons
DESeq2
updated 2 days ago by
Michael Love
42k • written 4 days ago by
Zainab
▴ 10
1
vote
0
replies
290
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
18 days ago
BioinfGuru
▴ 30
1
vote
2
replies
191
views
Improving the design matrices vignette in RNAseq123
RNAseq123
15 days ago • updated 1 day ago
Lluís Revilla Sancho
▴ 730
1
vote
1
reply
134
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 11 days ago by
Leo Lahti
▴ 40 • written 11 days ago by
Dario Strbenac
★ 1.5k
1
vote
1
reply
77
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 1 day ago by
Michael Love
42k • written 1 day ago by
mat149
▴ 70
1
vote
2
replies
199
views
Design Matrix within group comparison more than two groups
DESeq2
25 days ago • updated 24 days ago
hemantcnaik
• 0
1
vote
3
replies
216
views
Different Shrunk Log2FC according with reference
DESeq2
updated 13 days ago by
Michael Love
42k • written 13 days ago by
andrebolerbarros
▴ 20
1
vote
0
replies
207
views
News:
Nominations for Bioconductor Awards 2024!
Recognition
Awards
Bioconductor
Bioc204
6 weeks ago • updated 1 day ago
shepherl
3.9k
1
vote
2
replies
542
views
GSVA error
GSVA
23 days ago • updated 22 days ago
Alex
• 0
1
vote
2
replies
237
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
6 days ago • updated 5 days ago
Yveto
• 0
1
vote
2
replies
160
views
Error in champ.load(): The following specified files do not exist
ChAMP
20 days ago • updated 19 days ago
Sherin
• 0
1
vote
6
replies
495
views
GSVA on separate healthy and disease datasets
GSVA
updated 27 days ago by
James W. MacDonald
65k • written 28 days ago by
Lucy
▴ 60
1
vote
1
reply
179
views
Citation for edgeR user guide
edgeR
updated 14 days ago by
Gordon Smyth
50k • written 14 days ago by
k___
▴ 30
1
vote
1
reply
60
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
updated 7 hours ago by
James W. MacDonald
65k • written 7 hours ago by
zzrammal
• 0
1
vote
2
replies
718
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
20 days ago • updated 11 days ago
ussarizona
▴ 10
1
vote
2
replies
1000
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 14 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
1
reply
52
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 7 hours ago by
James W. MacDonald
65k • written 9 hours ago by
Abbey
• 0
1
vote
4
replies
335
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
13 days ago • updated 11 days ago
winwater0928
• 0
1
vote
1
reply
187
views
Differentially expressed genes in monocle pseudotime
monocle
updated 21 days ago by
Gordon Smyth
50k • written 23 days ago by
kthapa
• 0
1
vote
10
replies
458
views
Obtaining pheno data from CEL files
GEO
affy
5 weeks ago • updated 28 days ago
Kurtis
• 0
1
vote
3
replies
868
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 13 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
2
replies
336
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 3 days ago by
Gordon Smyth
50k • written 4 days ago by
Kim
• 0
1
vote
4
replies
483
views
DEseq2 coefficient
DESeq2
coefficient
10 weeks ago • updated 6 days ago
JKim
• 0
1
vote
1
reply
116
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
fernanda.backsouza
▴ 10
1
vote
2
replies
311
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
4 weeks ago • updated 4 days ago
Kim
• 0
1
vote
3
replies
352
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 22 days ago by
Gordon Smyth
50k • written 27 days ago by
Simran
• 0
1
vote
4
replies
238
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 15 days ago by
James W. MacDonald
65k • written 19 days ago by
Mirella Aurora
• 0
1
vote
2
replies
221
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
19 days ago
Le
• 0
1
vote
7
replies
1.8k
views
Error using champ.import
ChAMP
EPICv2
updated 20 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
1
vote
2
replies
245
views
How to retrieve detailed regression results from deseq2
DESeq2
27 days ago • updated 18 days ago
Weiqian
▴ 10
1
vote
7
replies
331
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
12 days ago • updated 11 days ago
pl23
• 0
1
vote
2
replies
142
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
21 days ago
Ana
• 0
0
votes
3
replies
259
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 19 days ago by
W. Evan Johnson
▴ 850 • written 25 days ago by
schlumbohm
• 0
0
votes
5
replies
303
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 13 days ago by
James W. MacDonald
65k • written 16 days ago by
Gayatri
• 0
0
votes
0
replies
69
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
7 days ago
Maria Doyle
▴ 70
0
votes
2
replies
223
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 27 days ago by
Michael Love
42k • written 4 weeks ago by
nhaus
▴ 30
0
votes
2
replies
921
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
0
votes
4
replies
270
views
DEG with low counts
DESeq2
updated 18 days ago by
Michael Love
42k • written 23 days ago by
Rajat
• 0
0
votes
0
replies
87
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
27 days ago
Dennis
• 0
0
votes
0
replies
79
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
8 days ago
Chris
• 0
0
votes
0
replies
135
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
27 days ago
Eryn
• 0
202 results • Page
2 of 5
Recent ...
Replies
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
nbay13
• 0
A little late to the party, but I found that using the equation you specified, the p-values are actually slightly off from base R's `t.test…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
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