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15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 2 days ago
Chris
• 0
6
votes
19
replies
2.4k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
12 days ago • updated 1 day ago
Chris
• 0
2
votes
9
replies
341
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 6 days ago by
James W. MacDonald
65k • written 7 days ago by
Alexandre
• 0
1
vote
7
replies
293
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
7 days ago • updated 6 days ago
pl23
• 0
5
votes
6
replies
2.7k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 2 hours ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 1 day ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
1
vote
4
replies
299
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
8 days ago • updated 6 days ago
winwater0928
• 0
3
votes
4
replies
165
views
Help with error using camera() in limma
CAMERA
limma
2 days ago • updated 1 day ago
Chris
• 0
0
votes
4
replies
237
views
Minfi - estimatecellscount
min
minfi
updated 3 days ago by
James W. MacDonald
65k • written 4 weeks ago by
clacarion
• 0
1
vote
4
replies
452
views
DEseq2 coefficient
DESeq2
coefficient
9 weeks ago • updated 1 day ago
JKim
• 0
0
votes
3
replies
154
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 2 days ago by
Alejandro Reyes
★ 1.9k • written 14 days ago by
Alessia
• 0
0
votes
3
replies
212
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 22 hours ago by
Michael Love
41k • written 1 day ago by
HAK
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 2 days ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
1
vote
3
replies
186
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 6 days ago by
Michael Love
41k • written 6 days ago by
JalapenoCornbread
• 0
0
votes
3
replies
89
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 8 hours ago by
ATpoint
★ 4.1k • written 20 hours ago by
james.zhang20
• 0
0
votes
3
replies
204
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 2 days ago by
James W. MacDonald
65k • written 3 days ago by
SSSJec
• 0
0
votes
3
replies
105
views
Store output of matchPWM()
biostrings
Biostrings
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
mat149
▴ 70
3
votes
3
replies
195
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 3 days ago by
ATpoint
★ 4.1k • written 3 days ago by
bioinf
▴ 10
2
votes
2
replies
1.0k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 2 days ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
0
votes
2
replies
30
views
DESeq2 v1.35.0
DESeq2
updated 2 hours ago by
Michael Love
41k • written 3 hours ago by
Espresso
• 0
0
votes
2
replies
149
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 9 days ago by
taur.vil
• 0
0
votes
2
replies
186
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
1 day ago • updated 18 hours ago
Yveto
• 0
2
votes
2
replies
166
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
3 days ago • updated 2 days ago
Chris
• 0
1
vote
2
replies
694
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
15 days ago • updated 6 days ago
ussarizona
▴ 10
0
votes
2
replies
81
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
1 day ago • updated 4 hours ago
Ian D.
▴ 70
0
votes
2
replies
181
views
PCA plot suggestions
DESeq2
PCAtools
updated 6 days ago by
Michael Love
41k • written 7 days ago by
Aaliya
• 0
0
votes
1
reply
203
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 2 days ago by
James W. MacDonald
65k • written 2 days ago by
SSSJec
• 0
1
vote
1
reply
150
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 6 days ago by
Gordon Smyth
50k • written 10 days ago by
Lluís Revilla Sancho
▴ 730
0
votes
1
reply
113
views
ATACseq merge peaks
DiffBind
updated 6 days ago by
ATpoint
★ 4.1k • written 8 days ago by
Shloka
• 0
1
vote
1
reply
106
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 5 days ago by
Leo Lahti
▴ 40 • written 6 days ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
82
views
putting my own expression data in deseq2
DESeq2
updated 2 days ago by
ATpoint
★ 4.1k • written 2 days ago by
Dev
• 0
0
votes
1
reply
59
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 2 days ago by
shepherl
3.9k • written 2 days ago by
bounlu
• 0
0
votes
1
reply
85
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
Agung
• 0
0
votes
1
reply
74
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
updated 2 days ago by
Michael Love
41k • written 2 days ago by
Aurora
• 0
1
vote
1
reply
77
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
marcusn
• 0
0
votes
1
reply
93
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 22 hours ago by
ATpoint
★ 4.1k • written 22 hours ago by
angelathuynh5
• 0
0
votes
1
reply
47
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
updated 9 hours ago by
ATpoint
★ 4.1k • written 20 hours ago by
kcarey
• 0
0
votes
1
reply
26
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 9 hours ago by
4r-rtg
• 0
3
votes
0
replies
39
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
23 hours ago
shepherl
3.9k
0
votes
0
replies
5
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
42 minutes ago
z_bahari
• 0
0
votes
0
replies
44
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
2 days ago
Maria Doyle
▴ 70
0
votes
0
replies
12
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
4 hours ago
Ian D.
▴ 70
0
votes
0
replies
13
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
4 hours ago • updated 3 hours ago
yvonneh
• 0
0
votes
0
replies
53
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
3 days ago
Chris
• 0
0
votes
0
replies
70
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
8 days ago • updated 3 days ago
Sara
• 0
0
votes
0
replies
8
views
flowStats for CyTOF
flowStats
1 hour ago
tholmes
• 0
0
votes
0
replies
54
views
Empty table plot using plotGseaTable()
fgsea
1 day ago • updated 22 hours ago
Chris
• 0
0
votes
0
replies
7
views
Gene-by-sample covariates in limma
Metabolomics
limma
41 minutes ago
c53aba27
• 0
49 results • Page
1 of 1
Recent ...
Replies
Answer: DESeq2 v1.35.0
by
Michael Love
41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i
by
James W. MacDonald
65k
Please don't piggyback on posts from 2.3 years ago. If you have a question, post as a new question.
Answer: DESeq2 v1.35.0
by
James W. MacDonald
65k
Odd release versions indicate a devel version, which upon release is incremented to the next even version, so you won't be able to find tha…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i
by
fatinataly
• 0
I tried also with oligo does not work, any other suggestion?
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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