1
vote
2
replies
336
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
5 weeks ago • updated 8 days ago Kim • 0
1
vote
2
replies
152
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
26 days ago Ana • 0
1
vote
2
replies
179
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
3 days ago • updated 2 days ago Dylan.Sheerin • 0
0
votes
1
reply
139
views
covariate with negative and positive values
DESeq2
updated 24 days ago by 42k • written 25 days ago by • 0
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 11 days ago by • 0 • written 7.9 years ago by • 0
1
vote
4
replies
345
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
18 days ago • updated 16 days ago winwater0928 • 0
0
votes
3
replies
278
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 10 days ago by 42k • written 11 days ago by • 0
0
votes
1
reply
122
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 12 days ago by 42k • written 12 days ago by • 0
1
vote
1
reply
192
views
Differentially expressed genes in monocle pseudotime
monocle
updated 26 days ago by 50k • written 28 days ago by • 0
1
vote
1
reply
145
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
updated 5 days ago by 65k • written 5 days ago by • 0
5
votes
6
replies
445
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 29 days ago by ★ 4.1k • written 4 weeks ago by ▴ 30
2
votes
2
replies
216
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
12 days ago Chris • 0
3
votes
3
replies
235
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 19 days ago by 42k • written 20 days ago by • 0
0
votes
3
replies
194
views
Store output of matchPWM()
biostrings Biostrings
updated 10 days ago by 65k • written 11 days ago by ▴ 70
1
vote
4
replies
498
views
DEseq2 coefficient
DESeq2 coefficient
11 weeks ago • updated 10 days ago JKim • 0
1
vote
2
replies
201
views
Design Matrix within group comparison more than two groups
DESeq2
4 weeks ago • updated 29 days ago hemantcnaik • 0
0
votes
1
reply
144
views
rlog transformation
DESeq2
updated 24 days ago by 42k • written 24 days ago by • 0
1
vote
1
reply
184
views
Citation for edgeR user guide
edgeR
updated 18 days ago by 50k • written 18 days ago by ▴ 30
4
votes
2
replies
589
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
9 days ago • updated 5 days ago gene_bioconductor ▴ 10
0
votes
3
replies
197
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 23 days ago by 50k • written 24 days ago by • 0
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma ebayes bayesian ls
updated 4 days ago by 50k • written 5.6 years ago by ▴ 10
0
votes
2
replies
148
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
12 days ago • updated 9 days ago Aurora • 0
1
vote
1
reply
109
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 6 days ago by 42k • written 6 days ago by ▴ 70
4
votes
6
replies
449
views
FilterByExpr low counts with small sample size
edgeR
25 days ago • updated 20 days ago Jonathan ▴ 10
0
votes
2
replies
923
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by • 0
1
vote
4
replies
215
views
minfi::read.metharray.exp
minfiData minfi
updated 18 days ago by ▴ 780 • written 20 days ago by • 0
0
votes
4
replies
293
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 19 hours ago by • 0 • written 11 days ago by ▴ 70
0
votes
1
reply
157
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 24 days ago by ★ 4.1k • written 25 days ago by • 0
0
votes
3
replies
177
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 12 days ago by ★ 1.9k • written 24 days ago by • 0
3
votes
1
reply
319
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 18 days ago by 42k • written 18 days ago by ▴ 40
0
votes
1
reply
144
views
SNP locus package for mouse?
SNPlocs packFinder
updated 26 days ago by 65k • written 28 days ago by • 0
1
vote
1
reply
119
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 5 days ago by 65k • written 5 days ago by • 0
1
vote
1
reply
141
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 15 days ago by ▴ 40 • written 16 days ago by ★ 1.5k
2
votes
5
replies
250
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 17 days ago by 65k • written 18 days ago by • 0
0
votes
1
reply
63
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 3 days ago by ★ 4.1k • written 3 days ago by • 0
0
votes
1
reply
118
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 24 days ago by 42k • written 24 days ago by • 0
1
vote
2
replies
167
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
18 days ago • updated 17 days ago ATpoint ★ 4.1k
0
votes
5
replies
309
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 18 days ago by 65k • written 20 days ago by • 0
0
votes
1
reply
133
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 9 days ago by 50k • written 9 days ago by • 0
2
votes
2
replies
192
views
fgsea significant result
fgsea
7 days ago • updated 6 days ago Chris • 0
1
vote
3
replies
226
views
Different Shrunk Log2FC according with reference
DESeq2
updated 18 days ago by 42k • written 18 days ago by ▴ 20
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 25 days ago by • 0 • written 11 months ago by • 0
3
votes
3
replies
253
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 13 days ago by ★ 4.1k • written 13 days ago by ▴ 10
5
votes
3
replies
278
views
Log-cpm values from limma
limma edgeR RNASeq
updated 2 days ago by 50k • written 24 days ago by • 0
0
votes
2
replies
806
views
Job: Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor artificialintelligence JobPosting machinelearning
written 8 months ago by 50k
6
votes
5
replies
458
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC minifi
written 10 weeks ago by • 0
1
vote
5
replies
494
views
Can't post a question containing code?
Bioconductor
updated 1 day ago by • 0 • written 3 months ago by ▴ 10
0
votes
1
reply
125
views
putting my own expression data in deseq2
DESeq2
updated 12 days ago by ★ 4.1k • written 12 days ago by • 0
0
votes
1
reply
250
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 11 days ago by 65k • written 12 days ago by • 0
0
votes
1
reply
150
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 9 days ago by 50k • written 9 days ago by • 0
191 results • Page 2 of 4
Recent ...
Replies
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ziliang • 0
I am so confused and frustrated learning to use this software. Isn't how you merge the peaksets one of the most important steps for the com…
Answer: SingleR Label.Ont by Denis • 0
[Jackpot City Casino][1] is the perfect option when looking for an online casino in Canada for an exciting vacation and huge winnings that …
Comment: deseq2 results by sajadahmad41454 • 0
thank you so much and sorry for bothering you again and again, it is urgent because it is my project deadline. i have removed that sample a…
Comment: deseq2 results by swbarnes2 ★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code? by NATASHA • 0
did you find a solution? I´m having the same problem
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
Awards • All
Popular Question to maria.soler • 0
Popular Question to Pietro ▴ 40
Popular Question to neilzhao ▴ 30
Popular Question to ATpoint ★ 4.1k
Teacher to Michael Love 42k
Locations • All
France, 28 minutes ago
United States, 41 minutes ago
WEHI, Melbourne, Australia, 49 minutes ago
Egypt, 1 hour ago
United Kingdom, 1 hour ago
Traffic: 462 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