Showing : rnaseq • reset
1
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8
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936
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 12 days ago by • 0
0
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0
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110
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
12 days ago brayas13 • 0
3
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11
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680
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 5 weeks ago by • 0
2
votes
4
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375
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
5 weeks ago jihoon.kim.1495 ▴ 10
1
vote
1
reply
242
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 6 weeks ago by 67k • written 6 weeks ago by • 0
1
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2
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427
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 7 weeks ago by 42k • written 7 weeks ago by ▴ 10
0
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3
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365
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
7 weeks ago Travis • 0
0
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5
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1.6k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.5 years ago by • 0
0
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2
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864
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 11 weeks ago by ★ 1.4k • written 11 weeks ago by • 0
3
votes
5
replies
888
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 3 months ago by ★ 1.4k • written 3 months ago by • 0
2
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3
replies
485
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
3 months ago BioinfGuru ▴ 70
3
votes
6
replies
785
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 3 months ago by • 0
4
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3
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1.2k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 4 months ago by ▴ 10
0
votes
3
replies
551
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 3 months ago by ★ 4.5k • written 3 months ago by • 0
1
vote
4
replies
1.4k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
4 months ago • updated 3 months ago Lucy ▴ 60
0
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4
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546
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 4 months ago by • 0
0
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0
replies
305
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
4 months ago JG13 • 0
0
votes
1
reply
348
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 5 months ago by 67k • written 5 months ago by • 0
1
vote
9
replies
1.3k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 5 months ago by 67k • written 5 months ago by ▴ 10
1
vote
3
replies
539
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 5 months ago by 67k • written 5 months ago by ▴ 50
2
votes
2
replies
607
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 5 months ago by ▴ 10 • written 6 months ago by • 0
0
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6
replies
1.2k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
5 months ago atan • 0
3
votes
2
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616
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
5 months ago mohammedtoufiq91 ▴ 10
0
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0
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276
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
6 months ago Bibi • 0
10
votes
11
replies
2.3k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 5 months ago by • 0 • written 7.2 years ago by ▴ 80
1
vote
3
replies
607
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 6 months ago by 51k • written 6 months ago by • 0
0
votes
3
replies
721
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 6 months ago by ★ 4.5k • written 6 months ago by • 0
0
votes
1
reply
466
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 6 months ago by 42k • written 6 months ago by • 0
0
votes
2
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432
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 6 months ago by • 0
0
votes
2
replies
557
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
7 months ago • updated 6 months ago catv • 0
5
votes
3
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813
views
Log-cpm values from limma
limma edgeR RNASeq
updated 6 months ago by 51k • written 7 months ago by • 0
0
votes
1
reply
538
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 7 months ago by 42k • written 7 months ago by • 0
0
votes
1
reply
469
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 7 months ago by ★ 4.5k • written 7 months ago by • 0
0
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2
replies
958
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
8 months ago kcarey • 0
2
votes
2
replies
500
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
8 months ago Sabiha ▴ 20
0
votes
2
replies
1.1k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
8 months ago kcarey • 0
1
vote
4
replies
536
views
DESeq2 Replicates
DESeq2 RNASeq
8 months ago kcarey • 0
1
vote
3
replies
641
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 8 months ago by ★ 1.4k • written 8 months ago by ▴ 10
0
votes
4
replies
644
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
8 months ago mperalc • 0
0
votes
2
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722
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 8 months ago by 51k • written 8 months ago by • 0
3
votes
5
replies
1.0k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 8 months ago by 42k • written 8 months ago by ▴ 10
2
votes
1
reply
481
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 8 months ago by 42k • written 8 months ago by ▴ 10
3
votes
6
replies
1.1k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
9 months ago • updated 8 months ago boczniak767 ▴ 740
0
votes
0
replies
490
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
9 months ago Abril • 0
2
votes
2
replies
977
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
9 months ago jackafiore • 0
1
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2
replies
1.7k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 18 months ago by • 0
0
votes
4
replies
690
views
Ballgown error in scan for c.tab files
ballgown RNASeq
9 months ago candacenewcome • 0
1
vote
3
replies
644
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
9 months ago island • 0
1
vote
3
replies
954
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 9 months ago by • 0
0
votes
1
reply
465
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 9 months ago by ▴ 210 • written 9 months ago by • 0
50 results • Page 1 of 1
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Replies
Comment: [How to construct a model.matrix ] by kyj2226 • 0
Thanks to you, I learn a lot. Many thanks, Yujin.
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
thank you for your advice, I posted separate post.
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by Robert Castelo ★ 3.4k
Hi, this is a long comment thread on 4-year old post, please open a new post with you question. To increase the odds of getting useful answ…
Answer: DESeq2 rerun returns different results by ATpoint ★ 4.5k
DESeq2 is deterministic if you use same input, code and software versions. Make sure to version-control your environment by at least tracki…
Answer: [How to construct a model.matrix ] by Gordon Smyth 51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Votes
Answer: [How to construct a model.matrix ]
C: DESeq2 baseMean values for each sample
C: DESeq2 baseMean values for each sample
Comment: ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$beta
A: Some questions for remove batch effect by using mnnCorrect
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