Showing : RNASEQ • reset
1
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157
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 11 hours ago by 42k • written 5 days ago by ▴ 10
0
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3
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174
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
3 days ago • updated 2 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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745
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 29 days ago by ★ 1.4k • written 4 weeks ago by • 0
3
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5
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698
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 6 weeks ago by ★ 1.4k • written 7 weeks ago by • 0
2
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3
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359
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
7 weeks ago • updated 6 weeks ago BioinfGuru ▴ 70
3
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6
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697
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 9 weeks ago by • 0
4
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3
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1.1k
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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 10 weeks ago by ▴ 10
0
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3
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476
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 9 weeks ago by ★ 4.4k • written 9 weeks ago by • 0
1
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4
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1.2k
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Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
11 weeks ago • updated 9 weeks ago Lucy ▴ 60
0
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4
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447
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 11 weeks ago by • 0
0
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0
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234
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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
299
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 3 months ago by 67k • written 3 months ago by • 0
1
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9
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975
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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 3 months ago by ▴ 10
1
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3
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453
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 3 months ago by 67k • written 3 months ago by ▴ 50
2
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2
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555
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 3 months ago by ▴ 10 • written 4 months ago by • 0
0
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6
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1.0k
views
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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502
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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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230
views
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
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3
replies
535
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 4 months ago by 51k • written 4 months ago by • 0
0
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3
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586
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 4 months ago by ★ 4.4k • written 5 months ago by • 0
0
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1
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370
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
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2
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380
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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
replies
479
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
5 months ago catv • 0
5
votes
3
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655
views
Log-cpm values from limma
limma edgeR RNASeq
updated 4 months ago by 51k • written 5 months ago by • 0
0
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1
reply
425
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
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1
reply
364
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 5 months ago by ★ 4.4k • written 5 months ago by • 0
0
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2
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763
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
6 months ago kcarey • 0
2
votes
2
replies
448
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
6 months ago Sabiha ▴ 20
0
votes
2
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839
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
6 months ago kcarey • 0
1
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4
replies
485
views
DESeq2 Replicates
DESeq2 RNASeq
6 months ago kcarey • 0
1
vote
3
replies
580
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 6 months ago by ★ 1.4k • written 7 months ago by ▴ 10
0
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4
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580
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
replies
643
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 7 months ago by 51k • written 7 months ago by • 0
3
votes
5
replies
930
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 6 months ago by 42k • written 7 months ago by ▴ 10
2
votes
1
reply
431
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 7 months ago by 42k • written 7 months ago by ▴ 10
3
votes
6
replies
992
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
7 months ago boczniak767 ▴ 740
0
votes
0
replies
444
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
7 months ago Abril • 0
2
votes
2
replies
822
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
7 months ago jackafiore • 0
1
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2
replies
1.6k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 17 months ago by • 0
0
votes
4
replies
628
views
Ballgown error in scan for c.tab files
ballgown RNASeq
8 months ago candacenewcome • 0
1
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3
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595
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
8 months ago island • 0
1
vote
3
replies
884
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
419
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
replies
941
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 7 months ago by 51k • written 8 months ago by • 0
3
votes
1
reply
525
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 8 months ago by 51k • written 8 months ago by • 0
0
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3
replies
909
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 8 months ago by • 0
0
votes
1
reply
459
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
8 months ago WS • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Poor dispersion fit in DESeq2 by Michael Love 42k
The fit (red line) doesn't matter because you have so many samples. Note there is almost no shrinkage. Besides that you may be intereste…
Answer: DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days p by Michael Love 42k
I'd recommend actually meeting with a local statistician to work out the analysis plan, or someone familiar with linear models in R. I h…
Answer: DESeq2 design and contrasts with 2 drug-treated and one control group by Michael Love 42k
> Now I am interested in comparing the DE genes between the resistant and acute groups, but I am unsure how to account for DMSO in that com…
Answer: Spectra and PSMatch- trouble in reducePSMs, joinSpectraData, or countIdentificat by Laurent Gatto 1.6k
Tthis happens because the sequence spectraVariable is expected to be an atomic vector or a List with elements of length 1, but it's not - s…
Comment: How should I run ssGSEA Hallmark Enrichment Analysis? by Ginny • 0
I think the other side of this question is that the non protein coding genes would be in the "background", they would influence the ranking…
Votes
Answer: ISO a solution to rank-order introns by transcript
Answer: ISO a solution to rank-order introns by transcript
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
Answer: addPatternDensity in 'qsea' takes too much time
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