0
votes
7
replies
400
views
DESeq filtering specific to contrasts
DESeq2
updated 12 days ago by 41k • written 10 weeks ago by • 0
0
votes
1
reply
136
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 16 days ago by • 0 • written 21 days ago by • 0
0
votes
3
replies
199
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 15 days ago by 41k • written 16 days ago by ▴ 20
0
votes
1
reply
57
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 1 day ago by 3.8k • written 2 days ago by • 0
0
votes
1
reply
82
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 1 day ago by 41k • written 2 days ago by • 0
0
votes
2
replies
233
views
Regressing out batch effects
DESeq2
updated 22 days ago by 41k • written 27 days ago by • 0
0
votes
1
reply
697
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 19 days ago by • 0 • written 11 months ago by • 0
0
votes
1
reply
199
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 1 day ago by 65k • written 2 days ago by • 0
2
votes
5
replies
235
views
get BM error
ensembldb
updated 7 days ago by 65k • written 8 days ago by • 0
0
votes
4
replies
5.1k
views
SingleR Label.Ont
SingleR
updated 16 days ago by • 0 • written 7 months ago by • 0
1
vote
6
replies
418
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 28 days ago by 41k • written 28 days ago by • 0
0
votes
3
replies
152
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 1 day ago by ★ 1.9k • written 14 days ago by • 0
2
votes
2
replies
379
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
20 days ago • updated 19 days ago Henry ▴ 10
2
votes
3
replies
315
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
17 days ago • updated 16 days ago daniel.carbajo • 0
3
votes
4
replies
162
views
Help with error using camera() in limma
CAMERA limma
1 day ago Chris • 0
1
vote
1
reply
102
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 8 days ago by 65k • written 8 days ago by ▴ 10
0
votes
1
reply
146
views
BAM write error in HTSeqGenie
HTSeqGenie BAM
updated 22 days ago by 65k • written 22 days ago by • 0
0
votes
2
replies
183
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
29 days ago • updated 28 days ago Gimena • 0
2
votes
2
replies
183
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 27 days ago by ★ 4.1k • written 27 days ago by ★ 1.5k
0
votes
1
reply
134
views
SNP locus package for mouse?
SNPlocs packFinder
updated 15 days ago by 65k • written 18 days ago by • 0
0
votes
2
replies
174
views
Gene Ontology doubt
microbiomeExplorer
4 weeks ago • updated 27 days ago Bhawna • 0
1
vote
1
reply
76
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 1 day ago by 41k • written 1 day ago by • 0
1
vote
2
replies
138
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
67
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
updated 1 day ago by 41k • written 2 days ago by • 0
1
vote
2
replies
129
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
15 days ago Ana • 0
8
votes
23
replies
912
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment ExpressionSet
updated 20 days ago by ★ 3.3k • written 21 days ago by ▴ 40
1
vote
4
replies
297
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
8 days ago • updated 6 days ago winwater0928 • 0
1
vote
1
reply
160
views
DESeq2 - Missing values in count matrix
DESeq2
updated 27 days ago by 65k • written 27 days ago by • 0
0
votes
3
replies
203
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 15 hours ago by 41k • written 1 day ago by • 0
1
vote
1
reply
180
views
Differentially expressed genes in monocle pseudotime
monocle
updated 16 days ago by 50k • written 18 days ago by • 0
3
votes
2
replies
200
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 10 days ago by ★ 3.9k • written 12 days ago by ▴ 10
2
votes
2
replies
167
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
20 days ago • updated 17 days ago daniel.carbajo • 0
1
vote
1
reply
106
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 5 days ago by ▴ 40 • written 6 days ago by ★ 1.5k
1
vote
2
replies
223
views
MethylKit read issue
methylKit
updated 26 days ago by 65k • written 4 weeks ago by • 0
4
votes
6
replies
396
views
FilterByExpr low counts with small sample size
edgeR
14 days ago • updated 9 days ago Jonathan ▴ 10
0
votes
4
replies
590
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 15 days ago by 41k • written 6 months ago by • 0
5
votes
6
replies
414
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 19 days ago by ★ 4.1k • written 22 days ago by ▴ 30
0
votes
3
replies
200
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 1 day ago by 65k • written 2 days ago by • 0
0
votes
4
replies
251
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 29 days ago by 41k • written 4 weeks ago by • 0
0
votes
1
reply
176
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 23 days ago by 65k • written 24 days ago by • 0
0
votes
2
replies
914
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by • 0
0
votes
2
replies
157
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 26 days ago by 65k • written 26 days ago by • 0
0
votes
2
replies
347
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
5 weeks ago • updated 29 days ago Gordon • 0
0
votes
1
reply
117
views
FDR via q-value
qvalue
updated 9 days ago by 65k • written 12 days ago by • 0
0
votes
3
replies
248
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 13 days ago by ▴ 850 • written 20 days ago by • 0
0
votes
0
replies
140
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
26 days ago andromeda • 0
1
vote
2
replies
206
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
14 days ago • updated 13 days ago Le • 0
2
votes
0
replies
30
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
16 hours ago shepherl 3.8k
0
votes
1
reply
550
views
CopywriteR output
CopywriteR
updated 26 days ago by • 0 • written 2.5 years ago by • 0
0
votes
3
replies
61
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 1 hour ago by ★ 4.1k • written 13 hours ago by • 0
204 results • Page 3 of 5
Recent ...
Replies
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq by james.zhang20 • 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Comment: Deseq2 and Normalization of RNA sequencing data by ATpoint ★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Awards • All
Popular Question to siajunren • 0
Scholar to Rory Stark ★ 5.2k
Popular Question to tangming2005 ▴ 190
Popular Question to Ian D. ▴ 70
Popular Question to junhui.li11 • 0
Locations • All
WEHI, Melbourne, Australia, 2 minutes ago
United States, 3 minutes ago
Spain, 3 minutes ago
France, 5 minutes ago
France, 7 minutes ago
Traffic: 805 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