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2
votes
2
replies
202
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
27 days ago
julia_mcdonough
• 0
2
votes
5
replies
766
views
DESeq2 setting significant p-value
DESeq2
updated 20 days ago by
Michael Love
42k • written 5.0 years ago by
Merlin
▴ 10
2
votes
5
replies
250
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 14 days ago by
James W. MacDonald
65k • written 16 days ago by
bandconductor
• 0
2
votes
2
replies
178
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
27 days ago • updated 24 days ago
daniel.carbajo
• 0
2
votes
3
replies
191
views
package goseq seems to be not available on the latest version of R
goseq
updated 3 days ago by
Gordon Smyth
50k • written 6 days ago by
Patrycja
▴ 20
2
votes
13
replies
439
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
18 days ago • updated 15 days ago
fernanda.backsouza
▴ 10
1
vote
4
replies
489
views
DEseq2 coefficient
DESeq2
coefficient
10 weeks ago • updated 8 days ago
JKim
• 0
1
vote
4
replies
247
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 17 days ago by
James W. MacDonald
65k • written 21 days ago by
Mirella Aurora
• 0
1
vote
2
replies
193
views
Improving the design matrices vignette in RNAseq123
RNAseq123
17 days ago • updated 3 days ago
Lluís Revilla Sancho
▴ 730
1
vote
3
replies
255
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 8 days ago by
angelathuynh5
• 0
1
vote
1
reply
93
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 3 days ago by
Michael Love
42k • written 3 days ago by
mat149
▴ 70
1
vote
4
replies
213
views
minfi::read.metharray.exp
minfiData
minfi
updated 15 days ago by
Basti
▴ 780 • written 17 days ago by
clacarion
• 0
1
vote
2
replies
576
views
GSVA error
GSVA
25 days ago • updated 24 days ago
Alex
• 0
1
vote
1
reply
130
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 9 days ago by
Michael Love
42k • written 9 days ago by
marcusn
• 0
1
vote
1
reply
138
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 13 days ago by
Leo Lahti
▴ 40 • written 13 days ago by
Dario Strbenac
★ 1.5k
1
vote
3
replies
872
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 15 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
1
reply
95
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 2 days ago by
James W. MacDonald
65k • written 2 days ago by
e1271094
• 0
1
vote
2
replies
165
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
15 days ago • updated 14 days ago
ATpoint
★ 4.1k
1
vote
3
replies
234
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 13 days ago by
Michael Love
42k • written 14 days ago by
JalapenoCornbread
• 0
1
vote
2
replies
164
views
Error in champ.load(): The following specified files do not exist
ChAMP
22 days ago • updated 21 days ago
Sherin
• 0
1
vote
2
replies
721
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
22 days ago • updated 13 days ago
ussarizona
▴ 10
1
vote
2
replies
246
views
How to retrieve detailed regression results from deseq2
DESeq2
29 days ago • updated 20 days ago
Weiqian
▴ 10
1
vote
0
replies
258
views
News:
Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition
Awards
Bioconductor
Bioc204
6 weeks ago • updated 10 hours ago
shepherl
3.9k
1
vote
2
replies
224
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
21 days ago
Le
• 0
1
vote
6
replies
500
views
GSVA on separate healthy and disease datasets
GSVA
updated 29 days ago by
James W. MacDonald
65k • written 4 weeks ago by
Lucy
▴ 60
1
vote
2
replies
249
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
8 days ago • updated 7 days ago
Yveto
• 0
1
vote
3
replies
353
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 24 days ago by
Gordon Smyth
50k • written 29 days ago by
Simran
• 0
1
vote
7
replies
338
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
14 days ago • updated 13 days ago
pl23
• 0
1
vote
1
reply
120
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 16 days ago by
James W. MacDonald
65k • written 16 days ago by
fernanda.backsouza
▴ 10
1
vote
2
replies
1.0k
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 16 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
2
replies
353
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 5 days ago by
Gordon Smyth
50k • written 6 days ago by
Kim
• 0
1
vote
2
replies
322
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
5 weeks ago • updated 6 days ago
Kim
• 0
1
vote
2
replies
147
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
23 days ago
Ana
• 0
1
vote
4
replies
341
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
15 days ago • updated 13 days ago
winwater0928
• 0
1
vote
1
reply
190
views
Differentially expressed genes in monocle pseudotime
monocle
updated 23 days ago by
Gordon Smyth
50k • written 25 days ago by
kthapa
• 0
1
vote
1
reply
104
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
James W. MacDonald
65k • written 2 days ago by
zzrammal
• 0
1
vote
2
replies
200
views
Design Matrix within group comparison more than two groups
DESeq2
27 days ago • updated 26 days ago
hemantcnaik
• 0
1
vote
3
replies
220
views
Different Shrunk Log2FC according with reference
DESeq2
updated 15 days ago by
Michael Love
42k • written 15 days ago by
andrebolerbarros
▴ 20
1
vote
1
reply
183
views
Citation for edgeR user guide
edgeR
updated 16 days ago by
Gordon Smyth
50k • written 16 days ago by
k___
▴ 30
1
vote
0
replies
304
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
20 days ago
BioinfGuru
▴ 30
1
vote
5
replies
1.5k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 1 day ago by
Jiayu
• 0 • written 5 months ago by
yanling
• 0
1
vote
7
replies
1.8k
views
Error using champ.import
ChAMP
EPICv2
updated 22 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
1
vote
1
reply
136
views
Handling multiple differential expression comparisons
DESeq2
updated 4 days ago by
Michael Love
42k • written 6 days ago by
Zainab
▴ 10
0
votes
1
reply
102
views
Input Question for deseq.r
RSeqAn
updated 21 days ago by
ATpoint
★ 4.1k • written 22 days ago by
Nina
• 0
0
votes
1
reply
140
views
rlog transformation
DESeq2
updated 21 days ago by
Michael Love
42k • written 21 days ago by
ishij9717
• 0
0
votes
0
replies
92
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
15 days ago • updated 10 days ago
Sara
• 0
0
votes
0
replies
107
views
Empty table plot using plotGseaTable()
fgsea
8 days ago • updated 6 days ago
Chris
• 0
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 3 days ago by
Caio
• 0 • written 13.1 years ago by
boczniak767
▴ 720
0
votes
3
replies
209
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 23 days ago by
Michael Love
42k • written 24 days ago by
andrebolerbarros
▴ 20
0
votes
1
reply
178
views
DESeq2 gives an error and R crashes
DESeq2
29 days ago • updated 28 days ago
Shefali
• 0
200 results • Page
2 of 4
Recent ...
Replies
Comment: Log-cpm values from limma
by
Gordon Smyth
50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Comment: Extremely small p-values using Limma for proteomic data
by
Abbey
• 0
This is the code. The only part I changed was adding the contrasts.fit as you suggested. Thanks for taking a look! ``` # Load necessary …
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
Probably. I would not expect such large fold changes. But without seeing your code, who knows?
Comment: Extremely small p-values using Limma for proteomic data
by
Abbey
• 0
Thank you James! This worked to fix the p-values. However, the plot still looks one-sided... any idea what's going on with the left side?…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
That ll be helpful. Thank you.
Votes
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
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
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