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Rnaseq
•
reset
1
vote
2
replies
157
views
Poor dispersion fit in DESeq2
limma
DESeq2
RNASeq
edgeR
updated 11 hours ago by
Michael Love
42k • written 5 days ago by
Ben
▴ 10
0
votes
3
replies
174
views
Meta-analysis on RNA-seq data sets
meta-analysis
sva
Combat_Seq
RNAseq
3 days ago • updated 2 days ago
Travis
• 0
0
votes
5
replies
1.6k
views
DESeq2 Multi-factor design not full rank
RNASeq
DESeq2
written 3.4 years ago by
jehimi
• 0
0
votes
2
replies
745
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq
DESeq2
updated 29 days ago by
swbarnes2
★ 1.4k • written 4 weeks ago by
Shwetal
• 0
3
votes
5
replies
698
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2
RNAseq
DifferentialExpression
updated 6 weeks ago by
swbarnes2
★ 1.4k • written 7 weeks ago by
BioNovice247
• 0
2
votes
3
replies
359
views
RUV - Does my data need further normalisation?
EDASeq
plotRLE
RNAseq
7 weeks ago • updated 6 weeks ago
BioinfGuru
▴ 70
3
votes
6
replies
697
views
A question occur when using DESeq2 on a complex design
DESeq2
rnaseqGene
RNASeq
written 9 weeks ago by
MedocRafael
• 0
4
votes
3
replies
1.1k
views
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
mila
▴ 10
0
votes
3
replies
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
ATpoint
★ 4.4k • written 9 weeks ago by
Mark
• 0
1
vote
4
replies
1.2k
views
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
votes
4
replies
447
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData
DEGraph
RNASeq
edgeR
DegNorm
written 11 weeks ago by
Shaozhen
• 0
0
votes
0
replies
234
views
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
James W. MacDonald
67k • written 3 months ago by
cbio
• 0
1
vote
9
replies
975
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2
clusterProfiler
Pathways
RNASeq
org.Mm.eg.db
updated 3 months ago by
James W. MacDonald
67k • written 3 months ago by
adrip
▴ 10
1
vote
3
replies
453
views
Including infectivity information to RNA-Seq analysis
RNASeqData
DESeq2
RNA-Seq
RNASeq
updated 3 months ago by
James W. MacDonald
67k • written 3 months ago by
Ben
▴ 50
2
votes
2
replies
555
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 3 months ago by
jessica.mcclintock
▴ 10 • written 4 months ago by
ttt
• 0
0
votes
6
replies
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
replies
502
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
4 months ago
mohammedtoufiq91
▴ 10
0
votes
0
replies
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
votes
11
replies
2.3k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 4 months ago by
Sara
• 0 • written 7.1 years ago by
Sylvain Foisy
▴ 80
1
vote
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
Gordon Smyth
51k • written 4 months ago by
Ashley
• 0
0
votes
3
replies
586
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 4 months ago by
ATpoint
★ 4.4k • written 5 months ago by
james.zhang20
• 0
0
votes
1
reply
370
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 5 months ago by
Michael Love
42k • written 5 months ago by
kcarey
• 0
0
votes
2
replies
380
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 5 months ago by
taur.vil
• 0
0
votes
2
replies
479
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
5 months ago
catv
• 0
5
votes
3
replies
655
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 4 months ago by
Gordon Smyth
51k • written 5 months ago by
Shaimaa Gamal
• 0
0
votes
1
reply
425
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 5 months ago by
Michael Love
42k • written 5 months ago by
09191919
• 0
0
votes
1
reply
364
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 5 months ago by
ATpoint
★ 4.4k • written 5 months ago by
Merav
• 0
0
votes
2
replies
763
views
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
replies
839
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
6 months ago
kcarey
• 0
1
vote
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
swbarnes2
★ 1.4k • written 7 months ago by
sap275
▴ 10
0
votes
4
replies
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
Gordon Smyth
51k • written 7 months ago by
ryann
• 0
3
votes
5
replies
930
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 6 months ago by
Michael Love
42k • written 7 months ago by
sap275
▴ 10
2
votes
1
reply
431
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 7 months ago by
Michael Love
42k • written 7 months ago by
sap275
▴ 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
vote
2
replies
1.6k
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 17 months ago by
informatician
• 0
0
votes
4
replies
628
views
Ballgown error in scan for c.tab files
ballgown
RNASeq
8 months ago
candacenewcome
• 0
1
vote
3
replies
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
georgii.vdovin
• 0
0
votes
1
reply
419
views
Error in GDCRNATools
ceRNA
GDCRNATools
RNASeq
updated 8 months ago by
Ram
▴ 210 • written 8 months ago by
Matvii Mykhailichenko
• 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
Gordon Smyth
51k • written 8 months ago by
Shaimaa Gamal
• 0
3
votes
1
reply
525
views
Dataset imbalance
RNASeq
DifferentialExpression
RnaSeqSampleSizeData
RnaSeqSampleSize
updated 8 months ago by
Gordon Smyth
51k • written 8 months ago by
Shaimaa Gamal
• 0
0
votes
3
replies
909
views
dittobarplot Var error
RNASeq
ditto
dittoSeq
SingleR
written 8 months ago by
Fayrouz
• 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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