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rnaseq
•
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0
votes
1
reply
102
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 7 days ago by
ATpoint
★ 4.0k • written 9 days ago by
Merav
• 0
0
votes
2
replies
191
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
28 days ago • updated 27 days ago
kcarey
• 0
2
votes
2
replies
233
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
4 weeks ago
Sabiha
▴ 20
0
votes
2
replies
223
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
5 weeks ago • updated 4 weeks ago
kcarey
• 0
1
vote
4
replies
279
views
DESeq2 Replicates
DESeq2
RNASeq
6 weeks ago
kcarey
• 0
1
vote
3
replies
324
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 6 weeks ago by
swbarnes2
★ 1.3k • written 6 weeks ago by
sap275
▴ 10
0
votes
4
replies
260
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
7 weeks ago • updated 6 weeks ago
mperalc
• 0
0
votes
2
replies
247
views
Error in featureCounts matrix
GenomeWideAssociation
countsimQC
RNASeq
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
ryann
• 0
3
votes
5
replies
583
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 6 weeks ago by
Michael Love
41k • written 7 weeks ago by
sap275
▴ 10
2
votes
1
reply
234
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 7 weeks ago by
Michael Love
41k • written 7 weeks ago by
sap275
▴ 10
3
votes
6
replies
484
views
Average biological replicates in RNA-seq
Mfuzz
RNASeq
8 weeks ago
boczniak767
▴ 720
0
votes
0
replies
186
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
9 weeks ago
Abril
• 0
2
votes
2
replies
354
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2
Normalization
RNASeq
10 weeks ago
jackafiore
• 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 11 months ago by
informatician
• 0
0
votes
4
replies
355
views
Ballgown error in scan for c.tab files
ballgown
RNASeq
11 weeks ago • updated 10 weeks ago
candacenewcome
• 0
1
vote
3
replies
312
views
DESeq2 analysis on time-series RNA experiment
RNASeqData
DESeq2
RNASeq
11 weeks ago
island
• 0
1
vote
3
replies
539
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics
Normalization
RNASeq
DESeq2
written 11 weeks ago by
georgii.vdovin
• 0
0
votes
1
reply
213
views
Error in GDCRNATools
ceRNA
GDCRNATools
RNASeq
updated 12 weeks ago by
Ram
▴ 190 • written 12 weeks ago by
Matvii Mykhailichenko
• 0
2
votes
4
replies
516
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
12 weeks ago
Sabiha
▴ 20
4
votes
6
replies
537
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 10 weeks ago by
Gordon Smyth
50k • written 3 months ago by
Shaimaa Gamal
• 0
3
votes
1
reply
245
views
Dataset imbalance
RNASeq
DifferentialExpression
RnaSeqSampleSizeData
RnaSeqSampleSize
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Shaimaa Gamal
• 0
0
votes
3
replies
430
views
dittobarplot Var error
RNASeq
ditto
dittoSeq
SingleR
written 3 months ago by
Fayrouz
• 0
0
votes
1
reply
245
views
DESeq Design for Time-Series Analysis
RNASeq
DESeq2
timecourse
3 months ago
WS
• 0
2
votes
3
replies
1.1k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 3 months ago by
swbarnes2
★ 1.3k • written 4 months ago by
Bo
• 0
1
vote
2
replies
415
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
3 months ago
Sabiha
▴ 20
1
vote
2
replies
408
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
4 months ago
drewhaydensteele
• 0
7
votes
2
replies
712
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
annikagable
• 0
0
votes
3
replies
427
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
4 months ago
Karthik
• 0
1
vote
1
reply
360
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq
DESeq2
updated 4 months ago by
Michael Love
41k • written 4 months ago by
pl23
• 0
2
votes
3
replies
437
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq
DESeq2
4 months ago
Karthik
• 0
2
votes
2
replies
383
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression
DESeq2
RNASeqData
RNASeq
StatisticalMethod
4 months ago
Manthos
• 0
2
votes
4
replies
578
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom
RNASeq
limma
5 months ago
Tyler Sagendorf
▴ 10
0
votes
1
reply
414
views
DESeq2 model for two genome system
RNASeq
DESeq2
updated 5 months ago by
Michael Love
41k • written 6 months ago by
Sean
• 0
0
votes
2
replies
507
views
TCGA counts to TPM from recount3 do not seem to right
recount3
TCGA
RNASeq
updated 5 months ago by
Leonardo Collado Torres
★ 1.0k • written 5 months ago by
tangming2005
▴ 190
0
votes
9
replies
2.4k
views
DESeq2 result really different when only use some sample vs all sample
deseq2
rnaseq
updated 5 months ago by
blowfish
• 0 • written 6.5 years ago by
bharata1803
▴ 60
1
vote
4
replies
589
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA
BatchEffect
RNASeq
limma
5 months ago
Wending
• 0
0
votes
0
replies
333
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST
KEGG
RNASeq
5 months ago
mch
• 0
4
votes
2
replies
568
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
alvaroperona1
▴ 10
0
votes
6
replies
788
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
5 months ago
erika.maldonado-rosado
• 0
0
votes
0
replies
316
views
is Dada2 biased toward a particular sequence ?
virology
dada2
amplican
Sequencing
RNASeq
6 months ago
Sara
• 0
0
votes
2
replies
616
views
Will DESeq2 be appropriate tool for analysis?
RNASeq
DESeq2
6 months ago • updated 5 months ago
Karthik
• 0
0
votes
0
replies
255
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
6 months ago
Florian
• 0
0
votes
0
replies
316
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam
pileup
Rsamtools
RNASeq
6 months ago
Xinqi
• 0
0
votes
0
replies
314
views
Using DADA2 for finding viral sequence variants
VariantDetection
dada2
RNASeq
6 months ago
Sara
• 0
1
vote
1
reply
391
views
Multiple comparison using DESeq2
RNASeqData
RNASeq
DESeq2
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
fuqichen1
• 0
1
vote
7
replies
791
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 4 months ago by
Gordon Smyth
50k • written 6 months ago by
Gimena
• 0
0
votes
2
replies
399
views
Issues with ddseq2 for treatment response factoring in different KO clones
Clonality
RNASeq
DESeq2
updated 6 months ago by
swbarnes2
★ 1.3k • written 6 months ago by
Jules
• 0
0
votes
1
reply
384
views
Comparing RNASeq data from multiple studies
RNASeqData
RnaSeqSampleSize
RNASeqPower
RNASeq
updated 6 months ago by
Basti
▴ 760 • written 6 months ago by
Luke
• 0
3
votes
5
replies
792
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 7 months ago by
ATpoint
★ 4.0k • written 7 months ago by
Shashank
• 0
1
vote
1
reply
431
views
bulk RNA-Seq batch correction
RNASeqData
rnaseqcomp
RNASeq
updated 7 months ago by
ATpoint
★ 4.0k • written 7 months ago by
jg0428
• 0
50 results • Page
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Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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