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RnaSeq
•
reset
5
votes
8
replies
22k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 6 months ago by
Ahdee
▴ 50 • written 2.6 years ago by
Mohamed
▴ 30
0
votes
9
replies
15k
views
How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2
pvalue
visualization
enhancedvolcano
rnaseq
written 6.0 years ago by
ricardo3889
• 0
0
votes
5
replies
10k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 11 months ago by
Eva
• 0 • written 8.4 years ago by
ctl
• 0
4
votes
16
replies
8.4k
views
Normalised counts from RUVg in RUVSeq
RUVg
ruvseq
rnaseq
updated 11 months ago by
Shaimaa Gamal
• 0 • written 9.8 years ago by
Pauly Lin
▴ 160
1
vote
6
replies
6.6k
views
GSVA on RNAseq data
gsva
rnaseq
updated 6 days ago by
Robert Castelo
★ 3.4k • written 5.9 years ago by
rocanja
▴ 60
3
votes
5
replies
4.8k
views
plotMDS in edgeR
edger
rnaseq
written 9.4 years ago by
gthm
▴ 30
10
votes
11
replies
2.5k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 9 months ago by
Sara
• 0 • written 7.5 years ago by
Sylvain Foisy
▴ 80
2
votes
5
replies
2.3k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR
RNASeq
RNASeqData
Bioconductor
written 24 months ago by
Rebekah
• 0
7
votes
3
replies
2.2k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
written 14 months ago by
annikagable
• 0
0
votes
5
replies
2.1k
views
EdgeR: paired samples together with independant samples
RNASeq
edgeR
RNASeq
edgeR
updated 10 months ago by
Gordon Smyth
52k • written 12.3 years ago by
Maria Keays
▴ 30
0
votes
2
replies
2.0k
views
Should immunoglobulin genes be filtered out during RNA-seq differential expression analysis
RNASeq
updated 11 months ago by
leedakyung1998
• 0 • written 3.5 years ago by
MP
• 0
1
vote
9
replies
1.9k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2
clusterProfiler
Pathways
RNASeq
org.Mm.eg.db
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
adrip
▴ 10
0
votes
5
replies
1.9k
views
DESeq2 Multi-factor design not full rank
RNASeq
DESeq2
written 3.8 years ago by
jehimi
• 0
0
votes
2
replies
1.8k
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
11 months ago
kcarey
• 0
0
votes
3
replies
1.7k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 7 months ago by
Arun
• 0 • written 2.3 years ago by
irvin.ng
• 0
1
vote
4
replies
1.6k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA
GSVAdata
RNAseq
7 months ago
Lucy
▴ 60
0
votes
6
replies
1.5k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq
Rsubread
9 months ago • updated 8 months ago
atan
• 0
1
vote
3
replies
1.4k
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 10 months ago by
Guangchuang Yu
★ 1.2k • written 23 months ago by
ruiqi.li
▴ 10
3
votes
6
replies
1.3k
views
Average biological replicates in RNA-seq
Mfuzz
RNASeq
12 months ago
boczniak767
▴ 740
1
vote
8
replies
1.3k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma
voom
RNASeq
edgeR
Microarray
written 3 months ago by
Adam Marstrand
• 0
0
votes
2
replies
1.3k
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
11 months ago
kcarey
• 0
3
votes
5
replies
1.3k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2
RNAseq
DifferentialExpression
updated 6 months ago by
swbarnes2
★ 1.4k • written 6 months ago by
BioNovice247
• 0
4
votes
3
replies
1.3k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2
RNAseq
written 7 months ago by
mila
▴ 10
3
votes
5
replies
1.3k
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 11 months ago by
Michael Love
43k • written 12 months ago by
sap275
▴ 10
0
votes
3
replies
1.2k
views
dittobarplot Var error
RNASeq
ditto
dittoSeq
SingleR
written 13 months ago by
Fayrouz
• 0
0
votes
4
replies
1.1k
views
Higher Dimensional RNASeq Clustering Significance
DESeq2
RNASeq
PrincipalComponent
pcaExplorer
written 2.2 years ago by
James
• 0
5
votes
3
replies
1.1k
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 9 months ago by
Gordon Smyth
52k • written 10 months ago by
Shaimaa Gamal
• 0
0
votes
2
replies
1.0k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq
DESeq2
updated 5 months ago by
swbarnes2
★ 1.4k • written 5 months ago by
Shwetal
• 0
1
vote
2
replies
956
views
Weird p-values using DESeq2?
DESeq2
RNASeq
updated 4 days ago by
ATpoint
★ 4.7k • written 4 days ago by
ingrid.h
• 0
0
votes
3
replies
943
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 9 months ago by
ATpoint
★ 4.7k • written 9 months ago by
james.zhang20
• 0
0
votes
4
replies
923
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq
DESeq2
24 days ago • updated 21 days ago
Quang NN
▴ 10
3
votes
11
replies
903
views
Highly DE genes but small count difference within conditions
RNASeq
DESeq2
RNASeqData
written 4 months ago by
bioshot.com
• 0
3
votes
6
replies
898
views
A question occur when using DESeq2 on a complex design
DESeq2
rnaseqGene
RNASeq
written 6 months ago by
MedocRafael
• 0
0
votes
2
replies
893
views
biomart not ound some prevous release
biomart
rnaseq
written 6.0 years ago by
jarod_v6@libero.it
▴ 40
0
votes
2
replies
880
views
Error in featureCounts matrix
GenomeWideAssociation
countsimQC
RNASeq
updated 11 months ago by
Gordon Smyth
52k • written 11 months ago by
ryann
• 0
1
vote
3
replies
783
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 11 months ago by
swbarnes2
★ 1.4k • written 11 months ago by
sap275
▴ 10
3
votes
2
replies
773
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
9 months ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
755
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 10 months ago by
Michael Love
43k • written 10 months ago by
09191919
• 0
0
votes
4
replies
738
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
11 months ago
mperalc
• 0
1
vote
3
replies
738
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 9 months ago by
Gordon Smyth
52k • written 9 months ago by
Ashley
• 0
2
votes
2
replies
715
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 8 months ago by
jessica.mcclintock
▴ 10 • written 9 months ago by
ttt
• 0
0
votes
2
replies
715
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
10 months ago
catv
• 0
2
votes
3
replies
685
views
RUV - Does my data need further normalisation?
EDASeq
plotRLE
RNAseq
6 months ago
BioinfGuru
▴ 70
0
votes
4
replies
684
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData
DEGraph
RNASeq
edgeR
DegNorm
written 7 months ago by
Shaozhen
• 0
1
vote
3
replies
663
views
Including infectivity information to RNA-Seq analysis
RNASeqData
DESeq2
RNA-Seq
RNASeq
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
Ben
▴ 50
0
votes
3
replies
651
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData
DESeq2
RNASeq
DifferentialExpression
updated 7 months ago by
ATpoint
★ 4.7k • written 7 months ago by
Mark
• 0
1
vote
4
replies
632
views
DESeq2 Replicates
DESeq2
RNASeq
11 months ago
kcarey
• 0
0
votes
1
reply
631
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 10 months ago by
ATpoint
★ 4.7k • written 10 months ago by
Merav
• 0
1
vote
5
replies
610
views
Deseq2 Design
RNASeq
DESeq2
updated 9 weeks ago by
James W. MacDonald
68k • written 9 weeks ago by
pm_25
• 0
0
votes
1
reply
598
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 10 months ago by
Michael Love
43k • written 10 months ago by
kcarey
• 0
50 results • Page
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