2
votes
2
replies
442
views
Limma : paired samples leading to unexpected estimates
limma
5 months ago Basti ▴ 780
2
votes
2
replies
543
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
5 months ago sandmann.t ▴ 70
0
votes
1
reply
220
views
muffz.plot2
Mfuzz
updated 5 months ago by 68k • written 5 months ago by • 0
0
votes
4
replies
942
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 4 months ago by 43k • written 5 months ago by • 0
1
vote
2
replies
436
views
Differential expression on the transcript-level
DESeq2
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
0
votes
3
replies
571
views
DEP R-package run_app ("TMT") spits this error: "Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'".
DEP
5 months ago • updated 4 months ago Shajahan • 0
3
votes
13
replies
2.2k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 14 months ago by • 0
3
votes
2
replies
940
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
5 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
620
views
MEDIPS.meth gives table with NA rpkm values
MEDIPS
updated 5 months ago by 68k • written 5 months ago by • 0
0
votes
1
reply
959
views
Using offset in edgeR
edgeR
updated 5 months ago by 53k • written 5 months ago by • 0
2
votes
2
replies
1.9k
views
ExperimentHub full metadata
ExperimentHub
written 6 months ago by ▴ 50
1
vote
2
replies
2.5k
views
Non-monotonic voomByGroup plot in Xenium data
XeniumIO voom
5 months ago richardallenfriedmanbrooklyn ▴ 30
0
votes
1
reply
649
views
cytolib uses outdated boost call
cytolib
updated 5 months ago by 68k • written 5 months ago by • 0
4
votes
8
replies
2.0k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
5 months ago richardallenfriedmanbrooklyn ▴ 30
0
votes
2
replies
353
views
can't post
devel
updated 5 months ago by 4.2k • written 5 months ago by • 0
7
votes
9
replies
5.7k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
5 months ago bbao ▴ 10
0
votes
1
reply
1.4k
views
How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray limma BRAIN Microarray limma BRAIN
updated 5 months ago by 53k • written 16.9 years ago by ▴ 10
0
votes
1
reply
558
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 5 months ago by 68k • written 5 months ago by • 0
3
votes
9
replies
4.6k
views
Best practice for handling large data (matrix with >2^31-1 non-zero elements) in SingleCellExperiment?
SingleCellExperiment
updated 8 weeks ago by • 0 • written 5 months ago by ▴ 10
0
votes
0
replies
247
views
News: Announcing a New Journal - Bioinformatics Methods and Applications - Now Open for Submissions
Bioconductor
5 months ago Wei Shi ★ 3.6k
1
vote
3
replies
2.4k
views
Regarding the issue of background genes in enrichment analysis
KEGG goTools seqTools
written 5 months ago by ▴ 10
0
votes
3
replies
2.4k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma Bioconductor Metabolomics
updated 5 months ago by 53k • written 6 months ago by • 0
2
votes
4
replies
3.3k
views
I would like to perform differential expression analysis of lncRNAs using DESeq2 and edgeR.
diffGeneAnalysis lncRNA
6 months ago John ▴ 10
0
votes
2
replies
1.0k
views
gene detection across experiments
DESeq2 Normalization
6 months ago Mara • 0
0
votes
3
replies
1.7k
views
RNA-seq: TPM batch effect correction
rnaseqDTU Normalization
updated 6 months ago by 68k • written 6 months ago by • 0
5
votes
11
replies
3.4k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 8 months ago by ▴ 10
0
votes
5
replies
2.0k
views
compute_fasta_digest does not match Salmon index hash
tximeta
written 9 months ago by • 0
0
votes
5
replies
922
views
WGCNA
WGCNA Normalization RNASeq
written 10 months ago by • 0
3
votes
4
replies
5.3k
views
Analysis of clusters of a heatmap with enrichGO of clusterProfiler: choice fo the categories to visualize
clusterProfiler enrichGO ComplexHeatmap
updated 6 months ago by 68k • written 6 months ago by ▴ 10
0
votes
3
replies
1.2k
views
TopGO question
topGO top
updated 6 months ago by 68k • written 6 months ago by • 0
0
votes
2
replies
1.1k
views
Starting with a clean bioconductor rstudio container
Bioconductor
updated 6 months ago by ★ 5.0k • written 6 months ago by • 0
0
votes
1
reply
2.4k
views
ChAMP pipeline error (champ.import)
software error
updated 6 months ago by • 0 • written 6.7 years ago by • 0
0
votes
2
replies
584
views
Problem in Chip-seq data analysis using MACS3
chipseq MACSdata
updated 6 months ago by ★ 5.0k • written 6 months ago by • 0
1
vote
5
replies
4.8k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 5 months ago by 43k • written 6 months ago by • 0
0
votes
1
reply
756
views
Which GTF file to use for creation of tx2gene files?
tximport
updated 6 months ago by 43k • written 6 months ago by • 0
1
vote
1
reply
2.2k
views
DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 6 months ago by 43k • written 6 months ago by • 0
0
votes
2
replies
1.2k
views
6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 6 months ago by 43k • written 6 months ago by • 0
0
votes
3
replies
1.0k
views
Many transcripts missing from tx2gene created from Ensembl GTF file
kallisto tximport ensembl
updated 6 months ago by • 0 • written 6 months ago by • 0
1
vote
2
replies
3.8k
views
Is voomByGroup available in limma?
limmaGUI voom
6 months ago richardallenfriedmanbrooklyn ▴ 30
0
votes
4
replies
1.8k
views
How to use goana function with zebrafish genome from org.Dr.eg.db
org.Dr.eg.db zebrafish limma
6 months ago Eric • 0
1
vote
3
replies
1.5k
views
News: Ensembl 114 / Ensembl Genomes 61 has been released!
biomaRt ensembldb
written 7 months ago by ▴ 30
0
votes
0
replies
25
views
Spam: wealthdt5
weaver wealth
6 months ago Enfurry 0
0
votes
0
replies
296
views
Y-axis break ihn Volcano Plot
EnhancedVolcano Y-axis_break Volcano_Plot
6 months ago rajdeepboral00 • 0
0
votes
0
replies
283
views
getQC(RGset.raw) from IlluminaHumanMethylationMSAmanifest
getQC hcg110.db
updated 6 months ago by 4.2k • written 6 months ago by • 0
3
votes
2
replies
1.5k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 6 months ago by ▴ 20
1
vote
2
replies
2.7k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 6 months ago by • 0
0
votes
0
replies
314
views
Job: Job: Ensembl Dataflow Coordinator
JobPosting ensembldb
6 months ago Aleena_Ensembl ▴ 30
0
votes
1
reply
1.4k
views
Retrieve Salmon transcript quantification file from recount3
recount3
updated 6 months ago by ★ 1.1k • written 7 months ago by ▴ 10
0
votes
1
reply
1.2k
views
error from library(IlluminaHumanMethylationMSAmanifest)
MSAarray25 hcg110.db
updated 6 months ago by 68k • written 6 months ago by • 0
0
votes
1
reply
915
views
Source / binary version mismatch for rGADEM
rGADEM
updated 6 months ago by 4.2k • written 6 months ago by • 0
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Error in SummarizedExperiment(assays = SimpleList(counts = countData)
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