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3
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14
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Once again a "Model matrix not full rank"
DESeq2
design
coldata
31 minutes ago • updated 10 minutes ago
arfranco
▴ 130
0
votes
0
replies
9
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
2 hours ago
gene_bioconductor
▴ 10
0
votes
0
replies
11
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
2 hours ago
z_bahari
• 0
0
votes
0
replies
14
views
Gene-by-sample covariates in limma
Metabolomics
limma
2 hours ago
c53aba27
• 0
0
votes
0
replies
10
views
flowStats for CyTOF
flowStats
4 hours ago
tholmes
• 0
0
votes
2
replies
40
views
DESeq2 v1.35.0
DESeq2
updated 4 hours ago by
Michael Love
41k • written 5 hours ago by
Espresso
• 0
0
votes
0
replies
15
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
6 hours ago
yvonneh
• 0
0
votes
0
replies
14
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
6 hours ago
Ian D.
▴ 70
0
votes
1
reply
28
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 11 hours ago by
4r-rtg
• 0
0
votes
2
replies
83
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
1 day ago • updated 6 hours ago
Ian D.
▴ 70
0
votes
1
reply
48
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
updated 11 hours ago by
ATpoint
★ 4.1k • written 22 hours ago by
kcarey
• 0
0
votes
3
replies
91
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 10 hours ago by
ATpoint
★ 4.1k • written 22 hours ago by
james.zhang20
• 0
0
votes
1
reply
94
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 1 day ago by
angelathuynh5
• 0
3
votes
0
replies
39
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
1 day ago
shepherl
3.9k
0
votes
0
replies
54
views
Empty table plot using plotGseaTable()
fgsea
1 day ago
Chris
• 0
0
votes
3
replies
107
views
Store output of matchPWM()
biostrings
Biostrings
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
mat149
▴ 70
0
votes
3
replies
214
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
HAK
• 0
0
votes
2
replies
188
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
1 day ago • updated 20 hours ago
Yveto
• 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
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
3
votes
4
replies
165
views
Help with error using camera() in limma
CAMERA
limma
2 days ago
Chris
• 0
1
vote
1
reply
78
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
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
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 3 days ago by
Agung
• 0
0
votes
0
replies
44
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
2 days ago
Maria Doyle
▴ 70
0
votes
1
reply
61
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
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
2
votes
2
replies
167
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
3 days ago
Chris
• 0
0
votes
3
replies
206
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
0
replies
54
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
3 days ago
Chris
• 0
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
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
2
replies
181
views
PCA plot suggestions
DESeq2
PCAtools
updated 6 days ago by
Michael Love
41k • written 7 days ago by
Aaliya
• 0
1
vote
3
replies
186
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 6 days ago by
Michael Love
41k • written 7 days ago by
JalapenoCornbread
• 0
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
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
1
vote
7
replies
293
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
7 days ago • updated 6 days ago
pl23
• 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 7 days ago by
James W. MacDonald
65k • written 7 days ago by
Alexandre
• 0
0
votes
0
replies
78
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
7 days ago
glaciya2018
• 0
1
vote
2
replies
140
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
8 days ago • updated 7 days ago
ATpoint
★ 4.1k
0
votes
1
reply
130
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 8 days ago by
Michael Love
41k • written 8 days ago by
kcarey
• 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
2
votes
5
replies
237
views
get BM error
ensembldb
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
Fara
• 0
2
votes
5
replies
214
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 7 days ago by
James W. MacDonald
65k • written 8 days ago by
bandconductor
• 0
0
votes
0
replies
73
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
8 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
201
views
Different Shrunk Log2FC according with reference
DESeq2
updated 8 days ago by
Michael Love
41k • written 8 days ago by
andrebolerbarros
▴ 20
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
1
reply
295
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 8 days ago by
Michael Love
41k • written 9 days ago by
i.sudbery
▴ 40
1
vote
1
reply
160
views
Citation for edgeR user guide
edgeR
updated 8 days ago by
Gordon Smyth
50k • written 9 days ago by
k___
▴ 30
0
votes
7
replies
684
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
9 weeks ago • updated 9 days ago
shepherl
3.9k
207 results • Page
1 of 5
Recent ...
Replies
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
numbers 1 to 3 represent observations and/or replicates Control is control. The three controls are shown as Control_1, control_2 and Contr…
Answer: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
The time and treatment are essentially the same thing, so you cannot have both in the model at the same time. Do the numbers 1:3 represent …
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.
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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