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rnaseqr
•
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7
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6
replies
3.4k
views
WHat is the difference between DEG and TopVarGenes in DESEq2?
DESeq2
R
RNASeqR
3.4 years ago
ecg1g15
▴ 20
6
votes
11
replies
3.9k
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 5 weeks ago by
Priya
• 0 • written 3.1 years ago by
Marina
▴ 40
5
votes
5
replies
2.4k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO
RNASeqR
Transcriptomics
updated 3.1 years ago by
James W. MacDonald
65k • written 3.1 years ago by
H. Z. Amini
▴ 10
4
votes
1
reply
1.9k
views
mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene
RNASeqR
DESeq2
RNAseq
updated 2.5 years ago by
Michael Love
41k • written 2.5 years ago by
sohail.mbio
▴ 10
3
votes
5
replies
2.0k
views
Volcano plot - select additional gene
EnhancedVolcano
RNASeqR
R
volcanoplot
updated 3.5 years ago by
Kevin Blighe
★ 3.9k • written 3.5 years ago by
camillab.
▴ 10
3
votes
4
replies
1.3k
views
GEO + RNA-seq. Total Newbie.
RNASeqData
RNASeq
GEO
RNASeqR
HELP
3.0 years ago
hgalmoore
• 0
2
votes
2
replies
1.4k
views
Need help in determing upregulated and downregulated genes
RNASeqR
3.0 years ago
Rishav
▴ 20
1
vote
2
replies
822
views
Bioconductor packages for doing tRNA seq analysis
RNASeqR
updated 3.1 years ago by
Gordon Smyth
50k • written 3.1 years ago by
Rishav
▴ 20
1
vote
10
replies
2.9k
views
Duplicate correlation with limma in before-after exposure experiment
RNASeqR
3.4 years ago • updated 2.9 years ago
sofie.haglund
• 0
1
vote
5
replies
867
views
Error when calculating DE using the classical approach in edgeR
RNASeqR
3.1 years ago
Rishav
▴ 20
1
vote
2
replies
1.4k
views
I am creating contrast matrix and i am following every procedure but still i don't understand where i am getting error
RNASeqR
3.1 years ago
Rishav
▴ 20
1
vote
2
replies
818
views
Error occured in designing a matrix
RNASeqR
updated 3.1 years ago by
Gordon Smyth
50k • written 3.1 years ago by
Rishav
▴ 20
1
vote
3
replies
873
views
Need help in doing network analysis using R
RNASeqR
updated 3.1 years ago by
ATpoint
★ 4.0k • written 3.1 years ago by
Rishav
▴ 20
1
vote
5
replies
1.5k
views
while designing matrix i got an error, please help me out
RNASeqR
updated 3.0 years ago by
Basti
▴ 760 • written 3.1 years ago by
Rishav
▴ 20
1
vote
3
replies
1.2k
views
Error with hclust
RNASeqR
#hclust
#wgcna
#dissimilarity
#average
updated 2.4 years ago by
ATpoint
★ 4.0k • written 2.4 years ago by
devbhavin20
• 0
1
vote
3
replies
1.7k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData
RNASeq
RNASeqR
3.0 years ago
dantasezequiel1
• 0
1
vote
1
reply
775
views
edgeR for SDE analysis
RNASeqRData
edgeR
RNASeqR
RNASeqData
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
vikycairoli
• 0
0
votes
1
reply
941
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 20 months ago by
Michael Love
41k • written 20 months ago by
estafana.t98
• 0
0
votes
3
replies
1.3k
views
using of z score in Differentially Expression Analysis
RNASeqR
updated 20 months ago by
ATpoint
★ 4.0k • written 20 months ago by
fatemehfakhari74
• 0
0
votes
1
reply
822
views
Question about normalizing and removing batch effects from bulk RNA-seq data from NCBI-SRA
Arabidopsis_thaliana_Data
RNASeqR
Normalization
BatchEffect
updated 2.5 years ago by
James W. MacDonald
65k • written 2.5 years ago by
bhandary.8590
▴ 20
0
votes
1
reply
906
views
Outliers on DESEq2 Results
RNASeqR
DifferentialExpression
DESeq2
updated 2.6 years ago by
Michael Love
41k • written 2.6 years ago by
Bruno Rodrigo
• 0
0
votes
2
replies
5.2k
views
TPM data in limma/voom
voom
limma
DifferentialExpression
edgeR
3.2 years ago • updated 3.1 years ago
RJM
• 0
0
votes
1
reply
739
views
Find significant genes related to a specific disease
GeneExpression
RNASeqR
limma
updated 3.4 years ago by
António Miguel de Jesus Domingues
▴ 490 • written 3.4 years ago by
Will
• 0
0
votes
1
reply
2.2k
views
Biological replicates in DESeq2
DESeq2
Bioconductor
RNASeqR
updated 3.1 years ago by
ATpoint
★ 4.0k • written 3.1 years ago by
Blanca
• 0
0
votes
2
replies
2.2k
views
Incorporating spike-ins to rna-seq analysis
Spike-in
RNASeqR
DESeq2
Normalization
rna-seq
updated 7 months ago by
manuel.fernandez
• 0 • written 2.0 years ago by
cicely.day
• 0
0
votes
1
reply
853
views
Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData
limma
RNASeq
RNASeqR
updated 3.0 years ago by
Gordon Smyth
50k • written 3.0 years ago by
Rita
• 0
0
votes
1
reply
1.0k
views
Using tximport to create the input for DESeq2
RNASeqR
updated 3.1 years ago by
Michael Love
41k • written 3.1 years ago by
ahmesalama
• 0
27 results • Page
1 of 1
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Replies
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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