Showing : rnaseq • reset
3
votes
11
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481
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 7 days ago by • 0
2
votes
4
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249
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
6 days ago • updated 5 days ago jihoon.kim.1495 ▴ 10
1
vote
1
reply
146
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 13 days ago by 67k • written 13 days ago by • 0
1
vote
2
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360
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 16 days ago by 42k • written 21 days ago by ▴ 10
0
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3
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301
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
18 days 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 3.4 years ago by • 0
0
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2
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781
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 6 weeks ago by ★ 1.4k • written 6 weeks ago by • 0
3
votes
5
replies
762
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 8 weeks ago by ★ 1.4k • written 9 weeks ago by • 0
2
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3
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409
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
9 weeks ago • updated 8 weeks ago BioinfGuru ▴ 70
3
votes
6
replies
730
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 11 weeks ago by • 0
4
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3
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1.2k
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DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 12 weeks ago by ▴ 10
0
votes
3
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492
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 11 weeks ago by ★ 4.5k • written 11 weeks ago by • 0
1
vote
4
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1.2k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
3 months ago • updated 12 weeks ago Lucy ▴ 60
0
votes
4
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489
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 3 months ago by • 0
0
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0
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248
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
3 months ago JG13 • 0
0
votes
1
reply
315
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 3 months ago by 67k • written 3 months ago by • 0
1
vote
9
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1.1k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 3 months ago by 67k • written 4 months ago by ▴ 10
1
vote
3
replies
483
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 4 months ago by 67k • written 4 months ago by ▴ 50
2
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2
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573
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 4 months ago by ▴ 10 • written 4 months ago by • 0
0
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6
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1.1k
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
4 months ago atan • 0
3
votes
2
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554
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
4 months ago mohammedtoufiq91 ▴ 10
0
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0
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244
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
4 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 4 months ago by • 0 • written 7.1 years ago by ▴ 80
1
vote
3
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562
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 5 months ago by 51k • written 5 months ago by • 0
0
votes
3
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610
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 5 months ago by ★ 4.5k • written 5 months ago by • 0
0
votes
1
reply
398
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 5 months ago by 42k • written 5 months ago by • 0
0
votes
2
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398
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 5 months ago by • 0
0
votes
2
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506
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
5 months ago catv • 0
5
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3
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716
views
Log-cpm values from limma
limma edgeR RNASeq
updated 5 months ago by 51k • written 5 months ago by • 0
0
votes
1
reply
473
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 5 months ago by 42k • written 5 months ago by • 0
0
votes
1
reply
406
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 6 months ago by ★ 4.5k • written 6 months ago by • 0
0
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2
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842
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
6 months ago kcarey • 0
2
votes
2
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469
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
7 months ago Sabiha ▴ 20
0
votes
2
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930
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
7 months ago kcarey • 0
1
vote
4
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504
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DESeq2 Replicates
DESeq2 RNASeq
7 months ago kcarey • 0
1
vote
3
replies
593
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 7 months ago by ★ 1.4k • written 7 months ago by ▴ 10
0
votes
4
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599
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
7 months ago mperalc • 0
0
votes
2
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668
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 7 months ago by 51k • written 7 months ago by • 0
3
votes
5
replies
967
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 7 months ago by 42k • written 7 months ago by ▴ 10
2
votes
1
reply
446
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 7 months ago by 42k • written 7 months ago by ▴ 10
3
votes
6
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1.0k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
7 months ago boczniak767 ▴ 740
0
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0
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460
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
8 months ago Abril • 0
2
votes
2
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873
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
8 months ago jackafiore • 0
1
vote
2
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1.7k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 17 months ago by • 0
0
votes
4
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649
views
Ballgown error in scan for c.tab files
ballgown RNASeq
8 months ago candacenewcome • 0
1
vote
3
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613
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
8 months ago island • 0
1
vote
3
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905
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 8 months ago by • 0
0
votes
1
reply
440
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 8 months ago by ▴ 210 • written 8 months ago by • 0
2
votes
4
replies
1.2k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
8 months ago Sabiha ▴ 20
4
votes
6
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967
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 8 months ago by 51k • written 9 months ago by • 0
50 results • Page 1 of 1
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Replies
Comment: How to reverse complement some elements of a DNAStringSet by Christine Jones • 0
Fantastic, thank you
Comment: When running contrasts, does it use normalized read counts? by Katherine • 0
Ok, so the comment I was given where they said DeSeq2 should be with normalized counts is incorrect. the ```normalized_counts``` variable …
Answer: How to reverse complement some elements of a DNAStringSet by James W. MacDonald 67k
You should always try the vectorized method first, rather than looping. ``` > myFasta[myFasta_rc] <- reverseComplement(myFasta[myFasta_…
Answer: When running contrasts, does it use normalized read counts? by James W. MacDonald 67k
A contrast is a comparison of two or more coefficients. When you run `nbiomWaldTest` you are fitting the GLM and estimating coefficients. T…
Comment: Too much data for Diffbind by Ou, Jianhong ★ 1.3k
Just in case if somebody still want to apply summits greater than 0 and got the same error, you can filter out the peaks with start positio…
Votes
Comment: featureCounts fails to load annotation file
Answer: How to reverse complement some elements of a DNAStringSet
Answer: KEGGgraph result difference
Answer: What should be the normalization protocol for RNA seq data for WGCNA?
What should be the normalization protocol for RNA seq data for WGCNA?
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