Showing : RNASEQ • reset
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 7 months ago by 50k • written 21 months ago by ▴ 30
7
votes
8
replies
11k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 11 months ago by ★ 4.0k • written 7.7 years ago by ▴ 20
25
votes
7
replies
10k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 6 months ago by ▴ 10 • written 6.5 years ago by ▴ 30
5
votes
7
replies
9.9k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 3 months ago by • 0 • written 7.1 years ago by • 0
0
votes
5
replies
9.2k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 4 weeks ago by • 0 • written 7.6 years ago by • 0
4
votes
16
replies
7.3k
views
Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 28 days ago by • 0 • written 8.9 years ago by ▴ 150
1
vote
9
replies
5.2k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 6.1 years ago by • 0
5
votes
15
replies
4.9k
views
Cross-species RNA-seq with DESeq2
deseq2 rnaseq across species
updated 10 months ago by 65k • written 6.8 years ago by ▴ 10
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.1 years ago by ▴ 40
4
votes
12
replies
3.7k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 6 months ago by • 0 • written 3.1 years ago by • 0
1
vote
8
replies
2.5k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 4 months ago by • 0 • written 3.3 years ago by ▴ 10
0
votes
9
replies
2.4k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 5 months ago by • 0 • written 6.5 years ago by ▴ 60
3
votes
11
replies
2.4k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
10 months ago Anna ▴ 20
4
votes
4
replies
2.0k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 4 months ago by 50k • written 2.3 years ago by ▴ 10
1
vote
4
replies
1.9k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 6 months ago by • 0 • written 3.1 years ago by • 0
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 17 days ago by 50k • written 11.5 years ago by ▴ 30
0
votes
1
reply
1.8k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 8 months ago by 65k • written 8 months ago by • 0
2
votes
8
replies
1.7k
views
Error in Create switchAnalyzeRlist
AlternativeSplicing RNASeq IsoformSwitchAnalyzeR gtf
written 20 months ago by ▴ 10
3
votes
1
reply
1.6k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 3 months ago by 50k • written 3.0 years ago by ▴ 60
0
votes
6
replies
1.5k
views
deseq2 pre filter rna seq
deseq2 rnaseq
updated 6 months ago by 41k • written 4.8 years ago by • 0
3
votes
12
replies
1.4k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 12 months ago by 41k • written 12 months ago by ▴ 10
1
vote
1
reply
1.4k
views
News: Bioinformatics Summer School - July 2019 - UCLouvain (Belgium)
RNAseq deseq2 proteomics transcriptomics workshop News
written 5.1 years ago by 1.6k
2
votes
5
replies
1.3k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 13 months ago by • 0
2
votes
5
replies
1.3k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
9 months ago • updated 8 months ago mohammedtoufiq91 ▴ 10
0
votes
2
replies
1.3k
views
Conducting pair-wise comparison in DESeq2?
DESeq2 deseq2 biocondu Bioconductor RNASeq
written 14 months ago by • 0
0
votes
2
replies
1.3k
views
Should immunoglobulin genes be filtered out during RNA-seq differential expression analysis
RNASeq
updated 5 weeks ago by • 0 • written 2.6 years ago by • 0
3
votes
2
replies
1.2k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 9 months ago by 50k • written 9 months ago by ▴ 10
2
votes
4
replies
1.1k
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 7 months ago by 41k • written 2.9 years ago by • 0
2
votes
3
replies
1.1k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 3 months ago by ★ 1.3k • written 4 months ago by • 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months ago by • 0
0
votes
2
replies
1.1k
views
model matrix not full rank
DESeq2 RNASeq
updated 11 months ago by • 0 • written 11 months ago by • 0
5
votes
7
replies
1.0k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 3 months ago by 50k • written 13 months ago by • 0
0
votes
2
replies
870
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 1 day ago by • 0 • written 17 months ago by • 0
0
votes
4
replies
869
views
Combine RNA-seq
BatchEffect R rnaseq
updated 12 months ago by ★ 1.3k • written 12 months ago by • 0
1
vote
6
replies
864
views
Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 8 months ago by ★ 4.0k • written 8 months ago by • 0
0
votes
3
replies
803
views
Account for heteroscedasticity when fitting gene expression data
RNAseq
updated 11 months ago by 41k • written 11 months ago by • 0
3
votes
5
replies
797
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
1
vote
7
replies
796
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 4 months ago by 50k • written 6 months ago by • 0
0
votes
6
replies
793
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
5 months ago erika.maldonado-rosado • 0
0
votes
3
replies
789
views
edgeR DEGs multilevel
edgeR RNASeq DifferentialRegulation
updated 11 months ago by 50k • written 11 months ago by • 0
1
vote
3
replies
775
views
Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 11 months ago by 50k • written 11 months ago by • 0
1
vote
2
replies
746
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 14 hours ago by • 0 • written 13 months ago by ▴ 10
5
votes
7
replies
736
views
Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 8 months ago by 50k • written 8 months ago by ▴ 10
7
votes
2
replies
718
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 4 months ago by 50k • written 4 months ago by • 0
3
votes
4
replies
691
views
Anova table edgeR limma
limma RNASeq edgeR
11 months ago KATHERINE CHUERE NUNES • 0
0
votes
2
replies
688
views
biomart not ound some prevous release
biomart rnaseq
written 5.2 years ago by ▴ 40
2
votes
1
reply
687
views
Grouping DEGs yields varying results
RNASeq limma
updated 8 months ago by 50k • written 8 months ago by ▴ 10
0
votes
2
replies
661
views
Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
9 months ago Matteo • 0
0
votes
3
replies
633
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 9 months ago by 65k • written 9 months ago by • 0
1
vote
2
replies
623
views
Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 11 months ago by 50k • written 11 months ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Finding DEGs by using edgeR by Gordon Smyth 50k
Filtering (removing lowly expressed genes) has nothing to do with normalization. It isn't clear why not subsetting would cause any difficu…
Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
Answer: How to make DGEList and design matrix by edgeR package by Gordon Smyth 50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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