15
votes
23
replies
2.1k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
8 weeks ago • updated 26 days ago Chris ▴ 10
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
5 weeks ago • updated 25 days ago Chris ▴ 10
10
votes
11
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 4 days ago by • 0 • written 6.8 years ago by ▴ 80
8
votes
6
replies
4.2k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler enrichplot
updated 3 days ago by ▴ 30 • written 5.1 years ago by ▴ 160
8
votes
41
replies
5.9k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 4 days ago by • 0 • written 5.5 years ago by ★ 4.0k
7
votes
6
replies
679
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
written 21 days ago by • 0
6
votes
19
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2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
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updated 26 days ago by • 0 • written 4.7 years ago by ▴ 10
5
votes
6
replies
359
views
Not able to install any Bioconductor 3.18 package [unable to access index]
Install
updated 3 days ago by ▴ 120 • written 3 days ago by ▴ 140
5
votes
3
replies
333
views
Log-cpm values from limma
limma edgeR RNASeq
updated 16 days ago by 50k • written 5 weeks ago by • 0
5
votes
6
replies
2.9k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 24 days ago by 66k • written 2.4 years ago by • 0
4
votes
9
replies
515
views
Memory errors using read.bismark?
dmrseq bsseq
6 weeks ago • updated 19 days ago Juan Higareda • 0
4
votes
3
replies
170
views
recount3 problem downloading data from source sra
recount3
updated 3 days ago by ★ 1.1k • written 5 days ago by ▴ 10
4
votes
5
replies
368
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
20 days ago • updated 11 days ago Chris ▴ 10
4
votes
2
replies
659
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
24 days ago • updated 20 days ago gene_bioconductor ▴ 10
4
votes
3
replies
1.0k
views
BayesSpace parameters for DLPFC Visium data
BayesSpace
written 3.1 years ago by ▴ 30
4
votes
0
replies
158
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
25 days ago shepherl 3.9k
4
votes
9
replies
330
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 10 days ago by ★ 4.2k • written 11 days ago by • 0
4
votes
9
replies
3.2k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 11 days ago by • 0 • written 5.2 years ago by ▴ 50
4
votes
11
replies
1.6k
views
can't open mghp.osn.xsede.org
GenomeInfoDbData genomeinfodbdata
updated 3 days ago by ▴ 120 • written 9 months ago by ▴ 60
3
votes
4
replies
307
views
Store output of matchPWM()
biostrings Biostrings
25 days ago • updated 12 days ago mat149 ▴ 70
3
votes
5
replies
331
views
Help with running egsea()
EGSEA
20 days ago • updated 18 days ago Chris ▴ 10
3
votes
3
replies
281
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 27 days ago by ★ 4.2k • written 27 days ago by ▴ 10
3
votes
10
replies
538
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 16 days ago by 66k • written 19 days ago by • 0
3
votes
7
replies
914
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 8 months ago by ▴ 10
3
votes
4
replies
280
views
Help with error using camera() in limma
CAMERA limma
26 days ago Chris ▴ 10
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma ebayes bayesian ls
updated 18 days ago by 50k • written 5.6 years ago by ▴ 10
3
votes
1
reply
165
views
How to save the DEXSeq results
DEXSeq
updated 20 days ago by 42k • written 20 days ago by • 0
2
votes
1
reply
156
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 20 days ago by 42k • written 20 days ago by ▴ 70
2
votes
1
reply
106
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 11 days ago by ★ 1.9k • written 13 days ago by • 0
2
votes
3
replies
202
views
Problem installing ChAMP on a MacBook
ChAMP
updated 10 days ago by 3.9k • written 10 days ago by • 0
2
votes
2
replies
101
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unable to access bioconductor packages - qvalue installation failed...
Install
updated 3 days ago by 3.9k • written 3 days ago by ▴ 10
2
votes
1
reply
215
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 19 days ago by 66k • written 19 days ago by • 0
2
votes
3
replies
314
views
package goseq seems to be not available on the latest version of R
goseq
updated 20 days ago by 50k • written 23 days ago by ▴ 20
2
votes
3
replies
1.8k
views
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 13 days ago by • 0 • written 3.6 years ago by ▴ 60
2
votes
3
replies
177
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 10 days ago by 50k • written 11 days ago by • 0
2
votes
3
replies
277
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 21 days ago by ★ 4.2k • written 23 days ago by • 0
2
votes
4
replies
159
views
Help with infinite recursion - non-zero exit status in installation of GenomeInfoDbData
Install GenomeInfoDbData GenomeInfoDb
updated 3 days ago by 66k • written 4 days ago by ▴ 20
2
votes
2
replies
304
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
19 days ago • updated 13 days ago zzrammal • 0
2
votes
2
replies
140
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
5 days ago • updated 4 days ago mohammedtoufiq91 ▴ 10
2
votes
7
replies
467
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
18 days ago • updated 15 days ago sajadahmad41454 • 0
2
votes
5
replies
277
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db Bioconductor
11 days ago • updated 9 days ago Patadù ▴ 10
2
votes
2
replies
438
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
14 days ago • updated 10 days ago Matthew Thornton ▴ 360
2
votes
4
replies
1.8k
views
slingshot: error with plot3d.SlingshotDataSet
slingshot plot3d.SlingshotDataSet
updated 4 days ago by • 0 • written 23 months ago by ▴ 10
2
votes
2
replies
252
views
fgsea significant result
fgsea
21 days ago Chris ▴ 10
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 26 days ago by • 0 • written 8.0 years ago by • 0
2
votes
2
replies
250
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
27 days ago Chris ▴ 10
2
votes
2
replies
83
views
Get gene symbols for a set of hg19 coordinates
annotation hg19
3 days ago pcantalupo ▴ 10
2
votes
4
replies
401
views
seqlevelsStyle() not working
ensembldb genomei GenomeInfoDb
written 3 months ago by ▴ 70
2
votes
4
replies
240
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 6 days ago by 42k • written 9 days ago by • 0
2
votes
4
replies
1.7k
views
EGSEA usage with microarray data (with vooma)?
EGSEA gene set testing vooma limma voom gsea
updated 17 days ago by ▴ 10 • written 7.4 years ago by ▴ 190
174 results • Page 1 of 4
Recent ...
Replies
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by BioinfGuru ▴ 30
I would use biomaRt. This is what happens when annotation occurs to early. If possible I would run the DEG analysis on the original output…
Comment: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0 by Maximus • 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Votes
A: Analyzing data without replicates using DiffBind
A: Analyzing data without replicates using DiffBind
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
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