Showing : RNASEQ • reset
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 11 days ago by • 0
0
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0
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107
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
11 days ago brayas13 • 0
3
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11
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676
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 5 weeks ago by • 0
2
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4
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370
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
5 weeks ago jihoon.kim.1495 ▴ 10
1
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1
reply
239
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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422
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 6 weeks ago by 42k • written 7 weeks ago by ▴ 10
0
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3
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360
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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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859
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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
884
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
479
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
3 months ago BioinfGuru ▴ 70
3
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6
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780
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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
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549
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
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4
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1.3k
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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543
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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
302
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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
346
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 5 months ago by 67k • written 5 months ago by • 0
1
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9
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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
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3
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538
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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
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2
replies
602
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 5 months ago by ▴ 10 • written 5 months ago by • 0
0
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6
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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
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2
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612
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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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273
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
6 months ago Bibi • 0
10
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11
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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
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3
replies
603
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
716
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
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1
reply
462
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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
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2
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428
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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
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2
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554
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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811
views
Log-cpm values from limma
limma edgeR RNASeq
updated 6 months ago by 51k • written 7 months ago by • 0
0
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1
reply
535
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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
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1
reply
463
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
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952
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
7 months ago kcarey • 0
2
votes
2
replies
497
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
8 months ago Sabiha ▴ 20
0
votes
2
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1.1k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
8 months ago kcarey • 0
1
vote
4
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529
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DESeq2 Replicates
DESeq2 RNASeq
8 months ago kcarey • 0
1
vote
3
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638
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 8 months ago by ★ 1.4k • written 8 months ago by ▴ 10
0
votes
4
replies
639
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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719
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 8 months ago by 51k • written 8 months ago by • 0
3
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5
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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
478
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 8 months ago by 42k • written 8 months ago by ▴ 10
3
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6
replies
1.1k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
9 months ago • updated 8 months ago boczniak767 ▴ 740
0
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0
replies
485
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
9 months ago Abril • 0
2
votes
2
replies
972
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
9 months ago jackafiore • 0
1
vote
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
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687
views
Ballgown error in scan for c.tab files
ballgown RNASeq
9 months ago candacenewcome • 0
1
vote
3
replies
639
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
9 months ago island • 0
1
vote
3
replies
953
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
462
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
Recent ...
Replies
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…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…
Comment: Merge Replicates vs Mixed Model by abadgerw • 0
@gabrielhoffman any insight?
Votes
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
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: [How to construct a model.matrix ]
Answer: Handling biological replicates in DESeq2
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