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0
replies
10
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
2 hours ago
Seungmin
• 0
0
votes
0
replies
35
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
16 hours ago
Matthew Thornton
▴ 350
0
votes
0
replies
37
views
The 'Home' shows:An error has occurred. Check your logs or contact the app author for clarification.
Reports
1 day ago
315005358
• 0
0
votes
1
reply
69
views
error
Biobase
1 day ago
NATASHA
• 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
34
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
2 days ago
neilzhao
▴ 30
0
votes
1
reply
63
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 3 days ago by
ATpoint
★ 4.1k • written 3 days ago by
sajadahmad41454
• 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
2
votes
7
replies
263
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
4 days ago • updated 1 day ago
sajadahmad41454
• 0
0
votes
0
replies
40
views
Treeio as.treedata function seq lenght error
treeio
4 days ago
nromerov
• 0
1
vote
1
reply
145
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
3
votes
10
replies
354
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 2 days ago by
James W. MacDonald
65k • written 5 days ago by
Abbey
• 0
0
votes
1
reply
75
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 5 days ago by
shepherl
3.9k • written 5 days ago by
cyril.dalmasso
• 0
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
0
votes
0
replies
57
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
5 days ago
Dinesh
• 0
3
votes
5
replies
233
views
Help with running egsea()
EGSEA
5 days ago • updated 4 days ago
Chris
• 0
3
votes
1
reply
114
views
How to save the DEXSeq results
DEXSeq
updated 6 days ago by
Michael Love
42k • written 6 days ago by
Sara
• 0
1
vote
1
reply
108
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 6 days ago by
Michael Love
42k • written 6 days ago by
mat149
▴ 70
0
votes
3
replies
161
views
Couldn't connect to server while using "pathways"
graphite
updated 5 days ago by
Michael Love
42k • written 6 days ago by
fduguchunhui
• 0
3
votes
4
replies
246
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
updated 4 days ago by
Gordon Smyth
50k • written 6 days ago by
Chris
• 0
3
votes
4
replies
468
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 4 days ago by
Mike Smith
★ 6.5k • written 6 days ago by
robersy
• 0
2
votes
2
replies
192
views
fgsea significant result
fgsea
7 days ago • updated 6 days ago
Chris
• 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
2
votes
3
replies
214
views
package goseq seems to be not available on the latest version of R
goseq
updated 6 days ago by
Gordon Smyth
50k • written 8 days ago by
Patrycja
▴ 20
2
votes
3
replies
216
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 7 days ago by
ATpoint
★ 4.1k • written 8 days ago by
Reza
• 0
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
0
votes
0
replies
101
views
dba.plotProfile() plotting and interpretation
DiffBind
8 days ago
Henry
▴ 10
0
votes
6
replies
252
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 8 days ago by
swbarnes2
★ 1.4k • written 9 days ago by
arfranco
▴ 130
4
votes
2
replies
589
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
9 days ago • updated 5 days ago
gene_bioconductor
▴ 10
0
votes
1
reply
149
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 9 days ago by
Gordon Smyth
50k • written 9 days ago by
z_bahari
• 0
0
votes
1
reply
133
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 9 days ago by
Gordon Smyth
50k • written 9 days ago by
c53aba27
• 0
0
votes
0
replies
78
views
flowStats for CyTOF
flowStats
9 days ago
tholmes
• 0
0
votes
2
replies
137
views
DESeq2 v1.35.0
DESeq2
updated 9 days ago by
Michael Love
42k • written 10 days ago by
Espresso
• 0
0
votes
0
replies
74
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
10 days ago
yvonneh
• 0
0
votes
0
replies
69
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
10 days ago
Ian D.
▴ 70
0
votes
1
reply
109
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 10 days ago by
4r-rtg
• 0
0
votes
2
replies
181
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
10 days ago • updated 9 days ago
kcarey
• 0
0
votes
3
replies
182
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 10 days ago by
ATpoint
★ 4.1k • written 10 days ago by
james.zhang20
• 0
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
4
votes
0
replies
113
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
10 days ago
shepherl
3.9k
0
votes
0
replies
123
views
Empty table plot using plotGseaTable()
fgsea
10 days ago • updated 8 days ago
Chris
• 0
0
votes
3
replies
194
views
Store output of matchPWM()
biostrings
Biostrings
updated 10 days ago by
James W. MacDonald
65k • written 11 days ago by
mat149
▴ 70
0
votes
4
replies
287
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 18 hours ago by
Ziliang
• 0 • written 11 days ago by
Ian D.
▴ 70
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
3
replies
278
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 10 days ago by
Michael Love
42k • written 11 days ago by
HAK
• 0
3
votes
4
replies
245
views
Help with error using camera() in limma
CAMERA
limma
12 days ago • updated 11 days ago
Chris
• 0
1
vote
1
reply
139
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 12 days ago by
Michael Love
42k • written 12 days ago by
marcusn
• 0
0
votes
0
replies
84
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
12 days ago
Maria Doyle
▴ 70
0
votes
1
reply
125
views
putting my own expression data in deseq2
DESeq2
updated 12 days ago by
ATpoint
★ 4.1k • written 12 days ago by
Dev
• 0
0
votes
2
replies
148
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
12 days ago • updated 9 days ago
Aurora
• 0
1,725 results • Page
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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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