0
votes
1
reply
11
views
Why p value inconsistent when using different number of pathway score?
limma
updated 20 minutes ago by ★ 4.0k • written 1 hour ago by • 0
15
votes
22
replies
1.7k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
21 days ago • updated 1 hour ago Chris • 0
0
votes
0
replies
9
views
I am trying to detect alternative splicing but getting error.
ASpli
2 hours ago Sebashish • 0
0
votes
0
replies
10
views
I am trying to detect alternative splicing.
ASpli
2 hours ago Sebashish • 0
3
votes
1
reply
1.4k
views
Job: Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job Job machine learning deep learning computational biology
written 6.3 years ago by ▴ 180
0
votes
2
replies
749
views
Job: Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor artificialintelligence JobPosting machinelearning
written 7 months ago by 50k
0
votes
4
replies
142
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
3 days ago • updated 9 hours ago lonn • 0
0
votes
1
reply
62
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 15 hours ago by ▴ 30 • written 18 hours ago by • 0
0
votes
1
reply
58
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
updated 16 hours ago by 50k • written 1 day ago by • 0
1
vote
1
reply
839
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate Gviz
updated 17 hours ago by ▴ 10 • written 13 months ago by ▴ 10
1
vote
2
replies
200
views
How to retrieve detailed regression results from deseq2
DESeq2
9 days ago • updated 21 hours ago Weiqian ▴ 10
1
vote
0
replies
112
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor Install
1 day ago • updated 22 hours ago BioinfGuru ▴ 30
0
votes
0
replies
30
views
FDR via q-value
qvalue
22 hours ago John • 0
0
votes
6
replies
564
views
News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
7 weeks ago • updated 23 hours ago shepherl 3.8k
0
votes
4
replies
198
views
FilterByExpr low counts with small sample size
edgeR
2 days ago • updated 1 day ago Jonathan ▴ 10
0
votes
7
replies
358
views
DESeq filtering specific to contrasts
DESeq2
updated 1 day ago by 41k • written 9 weeks ago by • 0
5
votes
14
replies
2.2k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by • 0 • written 4.6 years ago by ▴ 10
0
votes
2
replies
222
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
19 days ago • updated 1 day ago isaac.vock • 0
0
votes
3
replies
59
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 1 day ago by 65k • written 1 day ago by ▴ 30
2
votes
5
replies
673
views
DESeq2 setting significant p-value
DESeq2
updated 1 day ago by 41k • written 5.0 years ago by ▴ 10
1
vote
2
replies
78
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 1 day ago by 65k • written 1 day ago by • 0
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 1 day ago by • 0 • written 14 months ago by ▴ 10
0
votes
4
replies
205
views
DEG with low counts
DESeq2
updated 1 day ago by 41k • written 5 days ago by • 0
6
votes
5
replies
383
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC minifi
written 7 weeks ago by • 0
0
votes
3
replies
83
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 1 day ago by 50k • written 1 day ago by • 0
0
votes
2
replies
59
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
1 day ago prity6459 • 0
0
votes
1
reply
74
views
Log-cpm values from limma
limma edgeR RNASeq
updated 1 day ago by 50k • written 2 days ago by • 0
0
votes
2
replies
891
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by • 0
4
votes
8
replies
312
views
Memory errors using read.bismark?
dmrseq bsseq
updated 1 day ago by ▴ 740 • written 9 days ago by • 0
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA Theory Scale-Free Topology
updated 1 day ago by • 0 • written 9.1 years ago by ▴ 150
0
votes
4
replies
89
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
1 day ago sropri • 0
1
vote
2
replies
150
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
2 days ago • updated 1 day ago Le • 0
1
vote
2
replies
755
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 1 day ago by • 0 • written 13 months ago by ▴ 10
0
votes
0
replies
32
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
1 day ago Mirella Aurora • 0
0
votes
3
replies
201
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 1 day ago by ▴ 850 • written 8 days ago by • 0
0
votes
0
replies
49
views
Warning while loading DEP package
DEP
updated 1 day ago by 3.8k • written 2 days ago by • 0
0
votes
1
reply
54
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 1 day ago by ★ 1.9k • written 2 days ago by • 0
0
votes
1
reply
87
views
Adding columns to DEXSeqResults object
DEXSeq
updated 2 days ago by ★ 1.9k • written 3 days ago by • 0
0
votes
1
reply
59
views
rlog transformation
DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
0
votes
1
reply
56
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 2 days ago by 41k • written 2 days ago by • 0
0
votes
1
reply
65
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
0
votes
1
reply
82
views
covariate with negative and positive values
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
1
vote
2
replies
99
views
Error in champ.load(): The following specified files do not exist
ChAMP
2 days ago Sherin • 0
9
votes
12
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 2 days ago by • 0 • written 8.8 years ago by ▴ 30
5
votes
9
replies
815
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
9 days ago • updated 2 days ago Chris • 0
0
votes
1
reply
58
views
Input Question for deseq.r
RSeqAn
updated 2 days ago by ★ 4.0k • written 2 days ago by • 0
0
votes
1
reply
84
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 2 days ago by ★ 4.0k • written 3 days ago by • 0
3
votes
3
replies
146
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
8 days ago • updated 2 days ago jacques.imbert • 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 2 days ago by 50k • written 6 months ago by ▴ 10
0
votes
6
replies
163
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
updated 2 days ago by 50k • written 3 days ago by • 0
45,554 results • Page 1 of 912
Recent ...
Replies
Answer: Why p value inconsistent when using different number of pathway score? by ATpoint ★ 4.0k
Same answer as here: https://support.bioconductor.org/p/9157606/ Adding or removing data (samples, genes, pathways, observations...) chang…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Thanks Robert!
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Votes
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
Awards • All
Scholar to Robert Castelo ★ 3.2k
Popular Question to James W. MacDonald 65k
Popular Question to shepherl 3.8k
Popular Question to BioinfGuru ▴ 30
Popular Question to Gordon Smyth 50k
Locations • All
Estonia, 2 minutes ago
France/Marseille/Inserm, 12 minutes ago
Germany, 13 minutes ago
Germany, 15 minutes ago
France, 19 minutes ago
Traffic: 498 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