Showing : RnaSeq • reset
0
votes
2
replies
273
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 21 days ago by ★ 4.6k • written 26 days ago by • 0
1
vote
5
replies
499
views
Deseq2 Design
RNASeq DESeq2
updated 22 days ago by 67k • written 26 days ago by • 0
0
votes
2
replies
469
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 4 weeks ago by 52k • written 4 weeks ago by ▴ 10
0
votes
1
reply
171
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 6 weeks ago by ★ 4.6k • written 6 weeks ago by • 0
0
votes
5
replies
430
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 7 weeks ago by • 0
0
votes
1
reply
155
views
eRNAs count
RNASeq DESeq2
updated 7 weeks ago by ★ 4.6k • written 7 weeks ago by • 0
1
vote
8
replies
1.1k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 9 weeks ago by • 0
0
votes
0
replies
154
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
9 weeks ago brayas13 • 0
3
votes
11
replies
794
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 3 months ago by • 0
2
votes
4
replies
457
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
3 months ago jihoon.kim.1495 ▴ 10
1
vote
1
reply
351
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 3 months ago by 67k • written 3 months ago by • 0
1
vote
2
replies
494
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 3 months ago by 43k • written 3 months ago by ▴ 10
0
votes
3
replies
433
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
3 months ago Travis • 0
0
votes
5
replies
1.7k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.6 years ago by • 0
0
votes
2
replies
939
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 4 months ago by ★ 1.4k • written 4 months ago by • 0
3
votes
5
replies
1.1k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 4 months ago by ★ 1.4k • written 5 months ago by • 0
2
votes
3
replies
584
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
5 months ago • updated 4 months ago BioinfGuru ▴ 70
3
votes
6
replies
846
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 5 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 5 months ago by ▴ 10
0
votes
3
replies
602
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 5 months ago by ★ 4.6k • written 5 months ago by • 0
1
vote
4
replies
1.5k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
6 months ago • updated 5 months ago Lucy ▴ 60
0
votes
4
replies
622
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 6 months ago by • 0
0
votes
0
replies
364
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
6 months ago JG13 • 0
0
votes
1
reply
393
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 6 months ago by 67k • written 6 months ago by • 0
1
vote
9
replies
1.6k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 6 months ago by 67k • written 6 months ago by ▴ 10
1
vote
3
replies
600
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 7 months ago by 67k • written 7 months ago by ▴ 50
2
votes
2
replies
661
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 7 months ago by ▴ 10 • written 7 months ago by • 0
0
votes
6
replies
1.4k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
7 months ago atan • 0
3
votes
2
replies
699
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
7 months ago mohammedtoufiq91 ▴ 10
0
votes
0
replies
318
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
7 months ago Bibi • 0
10
votes
11
replies
2.4k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 7 months ago by • 0 • written 7.4 years ago by ▴ 80
1
vote
3
replies
677
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 7 months ago by 52k • written 7 months ago by • 0
0
votes
3
replies
845
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 8 months ago by ★ 4.6k • written 8 months ago by • 0
0
votes
1
reply
546
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 8 months ago by 43k • written 8 months ago by • 0
0
votes
2
replies
478
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 8 months ago by • 0
0
votes
2
replies
629
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
8 months ago catv • 0
5
votes
3
replies
959
views
Log-cpm values from limma
limma edgeR RNASeq
updated 8 months ago by 52k • written 8 months ago by • 0
0
votes
1
reply
634
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 8 months ago by 43k • written 8 months ago by • 0
0
votes
1
reply
569
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 9 months ago by ★ 4.6k • written 9 months ago by • 0
0
votes
2
replies
1.1k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
9 months ago kcarey • 0
2
votes
2
replies
551
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
10 months ago • updated 9 months ago Sabiha ▴ 20
0
votes
2
replies
1.5k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
10 months ago • updated 9 months ago kcarey • 0
1
vote
4
replies
581
views
DESeq2 Replicates
DESeq2 RNASeq
10 months ago kcarey • 0
1
vote
3
replies
723
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 10 months ago by ★ 1.4k • written 10 months ago by ▴ 10
0
votes
4
replies
692
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
10 months ago mperalc • 0
0
votes
2
replies
812
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 10 months ago by 52k • written 10 months ago by • 0
3
votes
5
replies
1.2k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 months ago by 43k • written 10 months ago by ▴ 10
2
votes
1
reply
513
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 10 months ago by 43k • written 10 months ago by ▴ 10
3
votes
6
replies
1.2k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
10 months ago boczniak767 ▴ 740
0
votes
0
replies
523
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
10 months ago Abril • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Newbie Question - adding metadata to an analysis by James W. MacDonald 67k
You don't need to generate an `ExpressionSet`, as you already have a `GeneFeatureSet`, which extends `eSet` and is a better fit for what yo…
Comment: Newbie Question - adding metadata to an analysis by Bryan H • 0
Thanks for the documentation. I have most of it working, except for the most critical step - incorporating the new metadata with the datase…
Comment: Diffbind interpretation of data - fold change by Vera • 0
Thank you for confirming that the foldchange is log2
Comment: Diffbind interpretation of data - fold change by Vera • 0
This solved it!
Comment: Diffbind interpretation of data - fold change by Vera • 0
Perfect! Thank you so much!
Votes
Answer: Considerations behind the choice of RNAseq Differential Expression Analysis Tool
A: goana limma- extract list of DE genes and genes in the enriched GO terms?
Answer: Package `not available for Bioconductor version '3.20'` when it should be
Comment: How do I fix an odd voom plot in a combined dataset?
Comment: How do I fix an odd voom plot in a combined dataset?
Awards • All
Popular Question to Dario Strbenac ★ 1.5k
Popular Question to Levi Waldron ★ 1.1k
Scholar to Michael Love 43k
Popular Question to Ken C • 0
Popular Question to gingergeiger22 • 0
Locations • All
United Kingdom, 2 minutes ago
Seattle, WA, United States, 47 minutes ago
Australia, 1 hour ago
Pakistan, 1 hour ago
Vietnam, 1 hour ago
Traffic: 581 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6