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3
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56
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Once again a "Model matrix not full rank"
DESeq2
design
coldata
6 hours ago
arfranco
▴ 130
0
votes
1
reply
117
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
updated 10 minutes ago by
Gordon Smyth
50k • written 8 hours ago by
gene_bioconductor
▴ 10
0
votes
1
reply
37
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 4 hours ago by
Gordon Smyth
50k • written 9 hours ago by
z_bahari
• 0
0
votes
1
reply
43
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 4 hours ago by
Gordon Smyth
50k • written 9 hours ago by
c53aba27
• 0
0
votes
0
replies
14
views
flowStats for CyTOF
flowStats
10 hours ago
tholmes
• 0
0
votes
2
replies
50
views
DESeq2 v1.35.0
DESeq2
updated 10 hours ago by
Michael Love
41k • written 11 hours ago by
Espresso
• 0
0
votes
0
replies
19
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
12 hours ago
yvonneh
• 0
0
votes
0
replies
15
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
12 hours ago
Ian D.
▴ 70
0
votes
1
reply
30
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 17 hours ago by
4r-rtg
• 0
0
votes
2
replies
71
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
1 day ago • updated 4 hours ago
kcarey
• 0
0
votes
3
replies
94
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 17 hours ago by
ATpoint
★ 4.1k • written 1 day ago by
james.zhang20
• 0
0
votes
1
reply
101
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
40
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
1 day ago
shepherl
3.9k
0
votes
0
replies
56
views
Empty table plot using plotGseaTable()
fgsea
1 day ago
Chris
• 0
0
votes
3
replies
114
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
2
replies
90
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
1 day ago • updated 12 hours ago
Ian D.
▴ 70
0
votes
2
replies
196
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
2 days ago • updated 1 day ago
Yveto
• 0
0
votes
3
replies
219
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
HAK
• 0
3
votes
4
replies
166
views
Help with error using camera() in limma
CAMERA
limma
2 days ago
Chris
• 0
1
vote
1
reply
81
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
0
replies
45
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
2 days ago
Maria Doyle
▴ 70
0
votes
1
reply
87
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
75
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
63
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
205
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 3 days ago by
SSSJec
• 0
0
votes
1
reply
86
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
2
votes
2
replies
169
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
0
replies
55
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
3 days ago
Chris
• 0
0
votes
3
replies
210
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
3
votes
3
replies
197
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
108
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 6 days ago by
Leo Lahti
▴ 40 • written 6 days ago by
Dario Strbenac
★ 1.5k
1
vote
3
replies
187
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 6 days ago by
Michael Love
41k • written 7 days ago by
JalapenoCornbread
• 0
1
vote
7
replies
295
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
7 days ago • updated 6 days ago
pl23
• 0
2
votes
9
replies
343
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
82
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
7 days ago
glaciya2018
• 0
0
votes
2
replies
182
views
PCA plot suggestions
DESeq2
PCAtools
updated 6 days ago by
Michael Love
41k • written 8 days ago by
Aaliya
• 0
0
votes
1
reply
135
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
1
reply
114
views
ATACseq merge peaks
DiffBind
updated 6 days ago by
ATpoint
★ 4.1k • written 8 days ago by
Shloka
• 0
0
votes
0
replies
72
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
8 days ago • updated 3 days ago
Sara
• 0
0
votes
0
replies
74
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
8 days ago
Dario Strbenac
★ 1.5k
1
vote
2
replies
141
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
8 days ago • updated 7 days ago
ATpoint
★ 4.1k
1
vote
3
replies
202
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
301
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
8 days ago • updated 6 days ago
winwater0928
• 0
2
votes
5
replies
240
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
215
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 7 days ago by
James W. MacDonald
65k • written 9 days ago by
bandconductor
• 0
1
vote
1
reply
161
views
Citation for edgeR user guide
edgeR
updated 9 days ago by
Gordon Smyth
50k • written 9 days ago by
k___
▴ 30
3
votes
1
reply
297
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 9 days ago by
Michael Love
41k • written 9 days ago by
i.sudbery
▴ 40
1
vote
1
reply
104
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 9 days ago by
James W. MacDonald
65k • written 9 days ago by
fernanda.backsouza
▴ 10
0
votes
8
replies
324
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 7 days ago by
swbarnes2
★ 1.3k • written 9 days ago by
Aaliya
• 0
0
votes
0
replies
65
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
9 days ago
info
▴ 10
206 results • Page
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Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
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.
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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