Showing : RnaSeq • reset
4
votes
16
replies
8.4k
views
Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 11 months ago by • 0 • written 9.8 years ago by ▴ 160
3
votes
11
replies
904
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 4 months ago by • 0
10
votes
11
replies
2.5k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 9 months ago by • 0 • written 7.5 years ago by ▴ 80
0
votes
2
replies
880
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 11 months ago by 52k • written 11 months ago by • 0
2
votes
2
replies
715
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 8 months ago by ▴ 10 • written 9 months ago by • 0
5
votes
8
replies
22k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 6 months ago by ▴ 50 • written 2.6 years ago by ▴ 30
0
votes
5
replies
10k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 11 months ago by • 0 • written 8.4 years ago by • 0
0
votes
4
replies
1.1k
views
Higher Dimensional RNASeq Clustering Significance
DESeq2 RNASeq PrincipalComponent pcaExplorer
written 2.2 years ago by • 0
0
votes
2
replies
1.0k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
0
votes
5
replies
1.9k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.8 years ago by • 0
4
votes
2
replies
440
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 9 weeks ago by ★ 4.7k • written 9 weeks ago by ▴ 10
1
vote
8
replies
1.3k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 3 months ago by • 0
3
votes
5
replies
1.3k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 6 months ago by ★ 1.4k • written 6 months ago by • 0
3
votes
2
replies
775
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
9 months ago mohammedtoufiq91 ▴ 10
0
votes
5
replies
586
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 3 months ago by • 0
4
votes
3
replies
1.3k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 7 months ago by ▴ 10
0
votes
3
replies
1.2k
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 13 months ago by • 0
2
votes
5
replies
2.3k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 24 months ago by • 0
7
votes
3
replies
2.2k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
written 14 months ago by • 0
0
votes
2
replies
715
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
10 months ago catv • 0
0
votes
3
replies
1.7k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 7 months ago by • 0 • written 2.3 years ago by • 0
1
vote
5
replies
611
views
Deseq2 Design
RNASeq DESeq2
updated 9 weeks ago by 68k • written 9 weeks ago by • 0
2
votes
4
replies
504
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
4 months ago jihoon.kim.1495 ▴ 10
0
votes
2
replies
2.0k
views
Should immunoglobulin genes be filtered out during RNA-seq differential expression analysis
RNASeq
updated 11 months ago by • 0 • written 3.5 years ago by • 0
1
vote
4
replies
632
views
DESeq2 Replicates
DESeq2 RNASeq
11 months ago kcarey • 0
2
votes
2
replies
589
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
11 months ago Sabiha ▴ 20
3
votes
5
replies
4.8k
views
plotMDS in edgeR
edger rnaseq
written 9.4 years ago by ▴ 30
0
votes
9
replies
15k
views
How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2 pvalue visualization enhancedvolcano rnaseq
written 6.0 years ago by • 0
0
votes
2
replies
894
views
biomart not ound some prevous release
biomart rnaseq
written 6.0 years ago by ▴ 40
1
vote
6
replies
6.6k
views
GSVA on RNAseq data
gsva rnaseq
updated 7 days ago by ★ 3.4k • written 5.9 years ago by ▴ 60
1
vote
2
replies
962
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 4 days ago by ★ 4.7k • written 5 days ago by • 0
2
votes
3
replies
685
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
6 months ago BioinfGuru ▴ 70
0
votes
3
replies
514
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 5 weeks ago by • 0
1
vote
1
reply
463
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 4 months ago by 68k • written 4 months ago by • 0
0
votes
1
reply
431
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 8 months ago by 68k • written 8 months ago by • 0
3
votes
6
replies
1.3k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
12 months ago boczniak767 ▴ 740
1
vote
3
replies
783
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 11 months ago by ★ 1.4k • written 11 months ago by ▴ 10
5
votes
3
replies
1.1k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 9 months ago by 52k • written 10 months ago by • 0
0
votes
1
reply
756
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 10 months ago by 43k • written 10 months ago by • 0
3
votes
6
replies
898
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 6 months ago by • 0
1
vote
3
replies
738
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 9 months ago by 52k • written 9 months ago by • 0
0
votes
2
replies
1.3k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
11 months ago kcarey • 0
0
votes
4
replies
925
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
24 days ago • updated 22 days ago Quang NN ▴ 10
0
votes
3
replies
340
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 16 days ago by • 0 • written 24 days ago by ▴ 10
0
votes
2
replies
515
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 10 weeks ago by 52k • written 10 weeks ago by ▴ 10
0
votes
2
replies
143
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
23 hours ago • updated 4 hours ago Marwan • 0
0
votes
3
replies
546
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
4 months ago Travis • 0
0
votes
1
reply
146
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 21 days ago by 43k • written 22 days ago by • 0
1
vote
2
replies
559
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 4 months ago by 43k • written 4 months ago by ▴ 10
1
vote
3
replies
663
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 8 months ago by 68k • written 8 months ago by ▴ 50
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to formulate 2 factor nested design in DESeq2 by Mariane • 0
Hi JK Kim, I'm having a problem similar to the one you reported. Could you please tell me how you solved this problem? Thanks
Comment: batch effect removal for agilent microarray data by gaye.yilmaz • 0
Thank you
Answer: Pathview visualisation not including positive log2 fold changes by James W. MacDonald 68k
Without providing a self-contained example, nobody can tell you if/where you went wrong. Since you get a KEGG pathway with some of the gene…
Comment: Differential variance analysis - can i use deseq2 by Marwan • 0
Thanks Michael for your answer, i didnt mean to use Deseq2 directly for the variance testing, but more like asking if using the (VST) data…
Answer: Differential variance analysis - can i use deseq2 by Michael Love 43k
We don't have a test of differential variance but other Bioconductor packages can, check similar posts (even on the right side bar) or use …
Votes
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
A: How to extract DESeq2 results for an interaction design
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
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