Showing : rnaseq • reset
25
votes
7
replies
11k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 7 months ago by ▴ 10 • written 6.6 years ago by ▴ 30
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 3 days ago by ▴ 220 • written 6.7 years ago by ▴ 80
7
votes
2
replies
864
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by 50k • written 5 months ago by • 0
6
votes
7
replies
797
views
Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 9 months ago by 50k • written 9 months ago by ▴ 10
5
votes
8
replies
4.0k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.2 years ago by ▴ 40
5
votes
3
replies
310
views
Log-cpm values from limma
limma edgeR RNASeq
updated 9 days ago by 50k • written 4 weeks ago by • 0
5
votes
7
replies
10k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 4 months ago by • 0 • written 7.2 years ago by • 0
5
votes
15
replies
5.1k
views
Cross-species RNA-seq with DESeq2
deseq2 rnaseq across species
updated 11 months ago by 65k • written 6.9 years ago by ▴ 10
5
votes
7
replies
1.1k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 4 months ago by 50k • written 14 months ago by • 0
4
votes
2
replies
1.3k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 10 months ago by 50k • written 10 months ago by ▴ 10
4
votes
16
replies
7.4k
views
Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 8 weeks ago by • 0 • written 9.0 years ago by ▴ 150
4
votes
12
replies
3.8k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 7 months ago by • 0 • written 3.2 years ago by • 0
4
votes
7
replies
14k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 8 months ago by 50k • written 22 months ago by ▴ 30
4
votes
2
replies
676
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 6 months ago by ▴ 10
4
votes
6
replies
643
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 4 months ago by • 0
4
votes
4
replies
2.1k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 5 months ago by 50k • written 2.4 years ago by ▴ 10
3
votes
1
reply
328
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 4 months ago by 50k • written 4 months ago by • 0
3
votes
1
reply
1.7k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 4 months ago by 50k • written 3.0 years ago by ▴ 60
3
votes
11
replies
2.6k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
11 months ago Anna ▴ 20
3
votes
5
replies
894
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
3
votes
6
replies
591
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
3 months ago • updated 12 weeks ago boczniak767 ▴ 720
3
votes
5
replies
670
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 weeks ago by 42k • written 12 weeks ago by ▴ 10
2
votes
4
replies
650
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
2
votes
5
replies
1.4k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
10 months ago • updated 9 months ago mohammedtoufiq91 ▴ 10
2
votes
1
reply
279
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 11 weeks ago by 42k • written 11 weeks ago by ▴ 10
2
votes
3
replies
523
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
5 months ago Karthik • 0
2
votes
3
replies
1.3k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 4 months ago by ★ 1.4k • written 5 months ago by • 0
2
votes
5
replies
1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
2
votes
2
replies
289
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 weeks ago Sabiha ▴ 20
2
votes
4
replies
1.2k
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 8 months ago by 42k • written 2.9 years ago by • 0
2
votes
4
replies
646
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
6 months ago Tyler Sagendorf ▴ 10
2
votes
8
replies
1.8k
views
Error in Create switchAnalyzeRlist
AlternativeSplicing RNASeq IsoformSwitchAnalyzeR gtf
written 21 months ago by ▴ 10
2
votes
1
reply
737
views
Grouping DEGs yields varying results
RNASeq limma
updated 9 months ago by 50k • written 9 months ago by ▴ 10
2
votes
2
replies
438
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
6 months ago • updated 5 months ago Manthos • 0
2
votes
2
replies
438
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago jackafiore • 0
1
vote
4
replies
2.0k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 7 months ago by • 0 • written 3.2 years ago by • 0
1
vote
3
replies
359
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 0
1
vote
4
replies
332
views
DESeq2 Replicates
DESeq2 RNASeq
10 weeks ago kcarey • 0
1
vote
3
replies
245
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 4 days ago by 50k • written 5 days ago by • 0
1
vote
7
replies
879
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 5 months ago by 50k • written 7 months ago by • 0
1
vote
4
replies
661
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
6 months ago Wending • 0
1
vote
2
replies
469
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago drewhaydensteele • 0
1
vote
8
replies
2.6k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 5 months ago by • 0 • written 3.4 years ago by ▴ 10
1
vote
2
replies
498
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
5 months ago • updated 4 months ago Sabiha ▴ 20
1
vote
2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
1
vote
3
replies
388
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 10 weeks ago by ★ 1.4k • written 11 weeks ago by ▴ 10
1
vote
1
reply
394
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 5 months ago by 42k • written 5 months ago by • 0
1
vote
3
replies
626
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 3 months ago by • 0
1
vote
1
reply
1.4k
views
News: Bioinformatics Summer School - July 2019 - UCLouvain (Belgium)
RNAseq deseq2 proteomics transcriptomics workshop News
written 5.2 years ago by 1.6k
1
vote
1
reply
476
views
bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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