0
votes
1
reply
15
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated just now by 50k • written 4 hours ago by • 0
0
votes
1
reply
20
views
Gene-by-sample covariates in limma
Metabolomics limma
updated just now by 50k • written 4 hours ago by • 0
0
votes
1
reply
32
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 20 minutes ago by 50k • written 3 hours ago by ▴ 10
0
votes
3
replies
38
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
2 hours ago • updated 1 hour ago arfranco ▴ 130
0
votes
0
replies
12
views
flowStats for CyTOF
flowStats
5 hours ago tholmes • 0
0
votes
2
replies
45
views
DESeq2 v1.35.0
DESeq2
updated 6 hours ago by 41k • written 7 hours ago by • 0
0
votes
0
replies
16
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
7 hours ago yvonneh • 0
0
votes
0
replies
15
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
7 hours ago Ian D. ▴ 70
0
votes
1
reply
29
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 12 hours ago by • 0
0
votes
2
replies
88
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
1 day ago • updated 7 hours ago Ian D. ▴ 70
0
votes
1
reply
49
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
updated 13 hours ago by ★ 4.1k • written 1 day ago by • 0
0
votes
3
replies
93
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 12 hours ago by ★ 4.1k • written 1 day ago by • 0
0
votes
1
reply
97
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 ★ 4.1k • written 1 day ago by • 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
55
views
Empty table plot using plotGseaTable()
fgsea
1 day ago Chris • 0
0
votes
3
replies
109
views
Store output of matchPWM()
biostrings Biostrings
updated 1 day ago by 65k • written 1 day ago by ▴ 70
0
votes
3
replies
217
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 1 day ago by 41k • written 2 days ago by • 0
0
votes
2
replies
192
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
1 day ago • updated 21 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 ▴ 200 • written 6.7 years ago by ▴ 80
0
votes
1
reply
204
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 65k • written 2 days ago by • 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 41k • written 2 days ago by • 0
0
votes
1
reply
75
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
updated 2 days ago by 41k • written 2 days ago by • 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 41k • written 3 days ago by • 0
0
votes
0
replies
45
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
2 days ago Maria Doyle ▴ 70
0
votes
1
reply
62
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 2 days ago by 3.9k • written 2 days ago by • 0
0
votes
1
reply
84
views
putting my own expression data in deseq2
DESeq2
updated 2 days ago by ★ 4.1k • written 2 days ago by • 0
2
votes
2
replies
168
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
207
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 65k • written 3 days ago by • 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
3
votes
3
replies
196
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 3 days ago by ★ 4.1k • written 3 days ago by ▴ 10
1
vote
1
reply
108
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 5 days ago by ▴ 40 • written 6 days ago by ★ 1.5k
0
votes
2
replies
182
views
PCA plot suggestions
DESeq2 PCAtools
updated 6 days ago by 41k • written 7 days ago by • 0
1
vote
3
replies
187
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 6 days ago by 41k • written 7 days ago by • 0
0
votes
1
reply
114
views
ATACseq merge peaks
DiffBind
updated 6 days ago by ★ 4.1k • written 8 days ago by • 0
1
vote
1
reply
151
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 6 days ago by 50k • written 10 days ago by ▴ 730
1
vote
7
replies
294
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
7 days ago • updated 6 days ago pl23 • 0
2
votes
9
replies
342
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 7 days ago by 65k • written 7 days ago by • 0
0
votes
0
replies
79
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
141
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
131
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 8 days ago by 41k • written 8 days ago by • 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
2
votes
5
replies
240
views
get BM error
ensembldb
updated 8 days ago by 65k • written 8 days ago by • 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 65k • written 9 days ago by • 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
3
replies
202
views
Different Shrunk Log2FC according with reference
DESeq2
updated 8 days ago by 41k • written 8 days ago by ▴ 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
3
votes
1
reply
297
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 8 days ago by 41k • written 9 days ago by ▴ 40
1
vote
1
reply
161
views
Citation for edgeR user guide
edgeR
updated 9 days ago by 50k • written 9 days ago by ▴ 30
0
votes
7
replies
686
views
News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
9 weeks ago • updated 9 days ago shepherl 3.9k
1,744 results • Page 1 of 35
Recent ...
Replies
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.
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 …
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
Awards • All
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Popular Question to shepherl 3.9k
Popular Question to siajunren • 0
Scholar to Rory Stark ★ 5.2k
Locations • All
WEHI, Melbourne, Australia, just now
France, 14 minutes ago
United States, 34 minutes ago
European Union, 1 hour ago
United States, 1 hour ago
Traffic: 578 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6