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Showing :
RNASeq
•
reset
0
votes
0
replies
22
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
14 hours ago
Bibi
• 0
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 3 days ago by
Leonard Goldstein
▴ 220 • written 6.7 years ago by
Sylvain Foisy
▴ 80
1
vote
3
replies
250
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 5 days ago by
Gordon Smyth
50k • written 6 days ago by
Ashley
• 0
0
votes
3
replies
225
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 17 days ago by
ATpoint
★ 4.1k • written 18 days ago by
james.zhang20
• 0
0
votes
1
reply
166
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 25 days ago by
Michael Love
42k • written 25 days ago by
kcarey
• 0
0
votes
2
replies
192
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 27 days ago by
taur.vil
• 0
0
votes
2
replies
242
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
4 weeks ago • updated 27 days ago
catv
• 0
5
votes
3
replies
313
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 9 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Shaimaa Gamal
• 0
0
votes
1
reply
128
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
09191919
• 0
0
votes
1
reply
155
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 5 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
Merav
• 0
0
votes
2
replies
269
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
8 weeks ago
kcarey
• 0
2
votes
2
replies
289
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
9 weeks ago
Sabiha
▴ 20
0
votes
2
replies
317
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
9 weeks ago
kcarey
• 0
1
vote
4
replies
332
views
DESeq2 Replicates
DESeq2
RNASeq
10 weeks ago
kcarey
• 0
1
vote
3
replies
388
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 10 weeks ago by
swbarnes2
★ 1.4k • written 11 weeks ago by
sap275
▴ 10
0
votes
4
replies
327
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
11 weeks ago
mperalc
• 0
0
votes
2
replies
346
views
Error in featureCounts matrix
GenomeWideAssociation
countsimQC
RNASeq
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
ryann
• 0
3
votes
5
replies
671
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 10 weeks ago by
Michael Love
42k • written 12 weeks ago by
sap275
▴ 10
2
votes
1
reply
281
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 11 weeks ago by
Michael Love
42k • written 11 weeks ago by
sap275
▴ 10
3
votes
6
replies
591
views
Average biological replicates in RNA-seq
Mfuzz
RNASeq
3 months ago • updated 12 weeks ago
boczniak767
▴ 720
0
votes
0
replies
242
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
3 months ago
Abril
• 0
2
votes
2
replies
439
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2
Normalization
RNASeq
3 months ago
jackafiore
• 0
1
vote
2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 12 months ago by
informatician
• 0
0
votes
4
replies
441
views
Ballgown error in scan for c.tab files
ballgown
RNASeq
3 months ago
candacenewcome
• 0
1
vote
3
replies
361
views
DESeq2 analysis on time-series RNA experiment
RNASeqData
DESeq2
RNASeq
3 months ago
island
• 0
1
vote
3
replies
626
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics
Normalization
RNASeq
DESeq2
written 3 months ago by
georgii.vdovin
• 0
0
votes
1
reply
260
views
Error in GDCRNATools
ceRNA
GDCRNATools
RNASeq
updated 3 months ago by
Ram
▴ 210 • written 3 months ago by
Matvii Mykhailichenko
• 0
2
votes
4
replies
651
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
4 months ago • updated 3 months ago
Sabiha
▴ 20
4
votes
6
replies
646
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 3 months ago by
Gordon Smyth
50k • written 4 months ago by
Shaimaa Gamal
• 0
3
votes
1
reply
329
views
Dataset imbalance
RNASeq
DifferentialExpression
RnaSeqSampleSizeData
RnaSeqSampleSize
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
Shaimaa Gamal
• 0
0
votes
3
replies
550
views
dittobarplot Var error
RNASeq
ditto
dittoSeq
SingleR
written 4 months ago by
Fayrouz
• 0
0
votes
1
reply
290
views
DESeq Design for Time-Series Analysis
RNASeq
DESeq2
timecourse
4 months ago
WS
• 0
2
votes
3
replies
1.3k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 4 months ago by
swbarnes2
★ 1.4k • written 5 months ago by
Bo
• 0
1
vote
2
replies
498
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
5 months ago
Sabiha
▴ 20
1
vote
2
replies
470
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
5 months ago
drewhaydensteele
• 0
7
votes
2
replies
864
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
0
votes
3
replies
481
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
5 months ago
Karthik
• 0
1
vote
1
reply
394
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq
DESeq2
updated 5 months ago by
Michael Love
42k • written 5 months ago by
pl23
• 0
2
votes
3
replies
524
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq
DESeq2
5 months ago
Karthik
• 0
2
votes
2
replies
439
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression
DESeq2
RNASeqData
RNASeq
StatisticalMethod
6 months ago
Manthos
• 0
2
votes
4
replies
646
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom
RNASeq
limma
6 months ago
Tyler Sagendorf
▴ 10
0
votes
1
reply
462
views
DESeq2 model for two genome system
RNASeq
DESeq2
updated 6 months ago by
Michael Love
42k • written 7 months ago by
Sean
• 0
0
votes
2
replies
564
views
TCGA counts to TPM from recount3 do not seem to right
recount3
TCGA
RNASeq
updated 6 months ago by
Leonardo Collado Torres
★ 1.0k • written 6 months ago by
tangming2005
▴ 190
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2
rnaseq
updated 6 months ago by
blowfish
• 0 • written 6.6 years ago by
bharata1803
▴ 60
1
vote
4
replies
663
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA
BatchEffect
RNASeq
limma
6 months ago
Wending
• 0
0
votes
0
replies
375
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST
KEGG
RNASeq
6 months ago
mch
• 0
4
votes
2
replies
681
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
alvaroperona1
▴ 10
0
votes
6
replies
921
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
6 months ago
erika.maldonado-rosado
• 0
0
votes
0
replies
352
views
is Dada2 biased toward a particular sequence ?
virology
dada2
amplican
Sequencing
RNASeq
7 months ago
Sara
• 0
0
votes
2
replies
663
views
Will DESeq2 be appropriate tool for analysis?
RNASeq
DESeq2
7 months ago • updated 6 months ago
Karthik
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
Galina
• 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
robersy
• 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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