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Views
Votes
2
votes
2
replies
175
views
[DiffBind] Obtaining normalization factors
DiffBind
29 days ago • updated 26 days ago
Henry
▴ 10
2
votes
2
replies
405
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
4 weeks ago • updated 29 days ago
Henry
▴ 10
2
votes
2
replies
216
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
12 days ago
Chris
• 0
2
votes
2
replies
199
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 23 days ago by
James W. MacDonald
65k • written 23 days ago by
sansan
• 0
2
votes
4
replies
1.7k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
updated 3 days ago by
Chris
• 0 • written 7.4 years ago by
Pekka Kohonen
▴ 190
1
vote
1
reply
123
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 18 days ago by
James W. MacDonald
65k • written 18 days ago by
fernanda.backsouza
▴ 10
1
vote
2
replies
228
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
24 days ago • updated 23 days ago
Le
• 0
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 19 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
3
replies
270
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 4 days ago by
ATpoint
★ 4.1k • written 10 days ago by
angelathuynh5
• 0
1
vote
2
replies
366
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 8 days ago by
Gordon Smyth
50k • written 8 days ago by
Kim
• 0
1
vote
4
replies
497
views
DEseq2 coefficient
DESeq2
coefficient
11 weeks ago • updated 10 days ago
JKim
• 0
1
vote
2
replies
201
views
Design Matrix within group comparison more than two groups
DESeq2
29 days ago
hemantcnaik
• 0
1
vote
2
replies
597
views
GSVA error
GSVA
28 days ago • updated 26 days ago
Alex
• 0
1
vote
2
replies
250
views
How to retrieve detailed regression results from deseq2
DESeq2
4 weeks ago • updated 22 days ago
Weiqian
▴ 10
1
vote
7
replies
1.8k
views
Error using champ.import
ChAMP
EPICv2
updated 24 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
1
vote
3
replies
238
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 16 days ago by
Michael Love
42k • written 16 days ago by
JalapenoCornbread
• 0
1
vote
1
reply
184
views
Citation for edgeR user guide
edgeR
updated 18 days ago by
Gordon Smyth
50k • written 18 days ago by
k___
▴ 30
1
vote
1
reply
151
views
Handling multiple differential expression comparisons
DESeq2
updated 7 days ago by
Michael Love
42k • written 8 days ago by
Zainab
▴ 10
1
vote
1
reply
119
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 5 days ago by
James W. MacDonald
65k • written 5 days ago by
e1271094
• 0
1
vote
3
replies
356
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 27 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Simran
• 0
1
vote
4
replies
215
views
minfi::read.metharray.exp
minfiData
minfi
updated 18 days ago by
Basti
▴ 780 • written 19 days ago by
clacarion
• 0
1
vote
1
reply
108
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 5 days ago by
Michael Love
42k • written 6 days ago by
mat149
▴ 70
1
vote
2
replies
336
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
5 weeks ago • updated 8 days ago
Kim
• 0
1
vote
2
replies
151
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
25 days ago
Ana
• 0
1
vote
2
replies
178
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
3 days ago • updated 2 days ago
Dylan.Sheerin
• 0
1
vote
0
replies
312
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
23 days ago • updated 22 days ago
BioinfGuru
▴ 30
1
vote
4
replies
254
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 19 days ago by
James W. MacDonald
65k • written 23 days ago by
Mirella Aurora
• 0
1
vote
2
replies
168
views
Error in champ.load(): The following specified files do not exist
ChAMP
24 days ago • updated 23 days ago
Sherin
• 0
1
vote
4
replies
345
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
18 days ago • updated 16 days ago
winwater0928
• 0
1
vote
3
replies
226
views
Different Shrunk Log2FC according with reference
DESeq2
updated 18 days ago by
Michael Love
42k • written 18 days ago by
andrebolerbarros
▴ 20
1
vote
5
replies
1.5k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 4 days ago by
Jiayu
• 0 • written 5 months ago by
yanling
• 0
1
vote
1
reply
141
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 15 days ago by
Leo Lahti
▴ 40 • written 16 days ago by
Dario Strbenac
★ 1.5k
1
vote
1
reply
192
views
Differentially expressed genes in monocle pseudotime
monocle
updated 26 days ago by
Gordon Smyth
50k • written 28 days ago by
kthapa
• 0
1
vote
1
reply
144
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
updated 4 days ago by
James W. MacDonald
65k • written 4 days ago by
zzrammal
• 0
1
vote
2
replies
167
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
18 days ago • updated 17 days ago
ATpoint
★ 4.1k
1
vote
1
reply
139
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 11 days ago by
Michael Love
42k • written 12 days ago by
marcusn
• 0
1
vote
7
replies
342
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
16 days ago • updated 15 days ago
pl23
• 0
1
vote
0
replies
278
views
News:
Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition
Awards
Bioconductor
Bioc204
7 weeks ago • updated 2 days ago
shepherl
3.9k
1
vote
3
replies
876
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 18 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
5
replies
494
views
Can't post a question containing code?
Bioconductor
updated 1 day ago by
NATASHA
• 0 • written 3 months ago by
DS
▴ 10
1
vote
2
replies
198
views
Improving the design matrices vignette in RNAseq123
RNAseq123
20 days ago • updated 6 days ago
Lluís Revilla Sancho
▴ 730
1
vote
2
replies
724
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
24 days ago • updated 15 days ago
ussarizona
▴ 10
1
vote
2
replies
263
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
11 days ago • updated 10 days ago
Yveto
• 0
0
votes
1
reply
71
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 2 days ago by
ATpoint
★ 4.1k • written 2 days ago by
sajadahmad41454
• 0
0
votes
0
replies
83
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
12 days ago
Maria Doyle
▴ 70
0
votes
4
replies
611
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 25 days ago by
Michael Love
42k • written 6 months ago by
Crystal571
• 0
0
votes
1
reply
156
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 26 days ago by
kamryncole1963
• 0 • written 4 weeks ago by
Sara
• 0
0
votes
1
reply
153
views
ATACseq merge peaks
DiffBind
updated 16 days ago by
ATpoint
★ 4.1k • written 17 days ago by
Shloka
• 0
0
votes
1
reply
111
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 12 days ago by
shepherl
3.9k • written 12 days ago by
bounlu
• 0
0
votes
1
reply
144
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 25 days ago by
James W. MacDonald
65k • written 28 days ago by
tian.liu0720
• 0
192 results • Page
2 of 4
Recent ...
Replies
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ziliang
• 0
I am so confused and frustrated learning to use this software. Isn't how you merge the peaksets one of the most important steps for the com…
Answer: SingleR Label.Ont
by
Denis
• 0
[Jackpot City Casino][1] is the perfect option when looking for an online casino in Canada for an exciting vacation and huge winnings that …
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you so much and sorry for bothering you again and again, it is urgent because it is my project deadline. i have removed that sample a…
Comment: deseq2 results
by
swbarnes2
★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code?
by
NATASHA
• 0
did you find a solution? I´m having the same problem
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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