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rnaseqr
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reset
6
votes
11
replies
5.1k
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 9 months ago by
Priya
• 0 • written 3.8 years ago by
Marina
▴ 40
1
vote
10
replies
3.4k
views
Duplicate correlation with limma in before-after exposure experiment
RNASeqR
4.0 years ago • updated 3.6 years ago
sofie.haglund
• 0
7
votes
6
replies
4.2k
views
WHat is the difference between DEG and TopVarGenes in DESEq2?
DESeq2
R
RNASeqR
4.0 years ago
ecg1g15
▴ 30
3
votes
5
replies
2.6k
views
Volcano plot - select additional gene
EnhancedVolcano
RNASeqR
R
volcanoplot
updated 4.1 years ago by
Kevin Blighe
★ 4.0k • written 4.1 years ago by
camillab.
▴ 10
5
votes
5
replies
3.1k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO
RNASeqR
Transcriptomics
updated 3.8 years ago by
James W. MacDonald
67k • written 3.8 years ago by
H. Z. Amini
▴ 10
1
vote
5
replies
1.9k
views
while designing matrix i got an error, please help me out
RNASeqR
updated 3.7 years ago by
Basti
▴ 780 • written 3.7 years ago by
Rishav
▴ 20
1
vote
5
replies
1.1k
views
Error when calculating DE using the classical approach in edgeR
RNASeqR
3.7 years ago
Rishav
▴ 20
3
votes
4
replies
1.7k
views
GEO + RNA-seq. Total Newbie.
RNASeqData
RNASeq
GEO
RNASeqR
HELP
3.7 years ago
hgalmoore
• 0
0
votes
3
replies
1.8k
views
using of z score in Differentially Expression Analysis
RNASeqR
updated 2.3 years ago by
ATpoint
★ 4.6k • written 2.3 years ago by
fatemehfakhari74
• 0
1
vote
3
replies
1.4k
views
Error with hclust
RNASeqR
#hclust
#wgcna
#dissimilarity
#average
updated 3.0 years ago by
ATpoint
★ 4.6k • written 3.0 years ago by
devbhavin20
• 0
1
vote
3
replies
1.1k
views
Need help in doing network analysis using R
RNASeqR
updated 3.7 years ago by
ATpoint
★ 4.6k • written 3.7 years ago by
Rishav
▴ 20
1
vote
3
replies
2.2k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData
RNASeq
RNASeqR
3.6 years ago
dantasezequiel1
• 0
0
votes
2
replies
3.1k
views
Incorporating spike-ins to rna-seq analysis
Spike-in
RNASeqR
DESeq2
Normalization
rna-seq
updated 15 months ago by
manuel.fernandez
• 0 • written 2.7 years ago by
cicely.day
• 0
0
votes
2
replies
6.7k
views
TPM data in limma/voom
voom
limma
DifferentialExpression
edgeR
3.8 years ago
RJM
• 0
1
vote
2
replies
1.9k
views
I am creating contrast matrix and i am following every procedure but still i don't understand where i am getting error
RNASeqR
3.7 years ago
Rishav
▴ 20
1
vote
2
replies
990
views
Error occured in designing a matrix
RNASeqR
updated 3.7 years ago by
Gordon Smyth
52k • written 3.7 years ago by
Rishav
▴ 20
1
vote
2
replies
968
views
Bioconductor packages for doing tRNA seq analysis
RNASeqR
updated 3.7 years ago by
Gordon Smyth
52k • written 3.7 years ago by
Rishav
▴ 20
2
votes
2
replies
2.0k
views
Need help in determing upregulated and downregulated genes
RNASeqR
3.6 years ago
Rishav
▴ 20
0
votes
1
reply
2.8k
views
Biological replicates in DESeq2
DESeq2
Bioconductor
RNASeqR
updated 3.8 years ago by
ATpoint
★ 4.6k • written 3.8 years ago by
Blanca
• 0
0
votes
1
reply
1.1k
views
Question about normalizing and removing batch effects from bulk RNA-seq data from NCBI-SRA
Arabidopsis_thaliana_Data
RNASeqR
Normalization
BatchEffect
updated 3.2 years ago by
James W. MacDonald
67k • written 3.2 years ago by
bhandary.8590
▴ 20
0
votes
1
reply
1.1k
views
Outliers on DESEq2 Results
RNASeqR
DifferentialExpression
DESeq2
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
Bruno Rodrigo
• 0
4
votes
1
reply
2.5k
views
mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene
RNASeqR
DESeq2
RNAseq
updated 3.1 years ago by
Michael Love
43k • written 3.1 years ago by
sohail.mbio
▴ 10
0
votes
1
reply
868
views
Find significant genes related to a specific disease
GeneExpression
RNASeqR
limma
updated 4.0 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 4.0 years ago by
Will
• 0
1
vote
1
reply
982
views
edgeR for SDE analysis
RNASeqRData
edgeR
RNASeqR
RNASeqData
updated 2.8 years ago by
Gordon Smyth
52k • written 2.8 years ago by
vikycairoli
• 0
0
votes
1
reply
1.4k
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 2.3 years ago by
Michael Love
43k • written 2.3 years ago by
estafana.t98
• 0
0
votes
1
reply
1.3k
views
Using tximport to create the input for DESeq2
RNASeqR
updated 3.8 years ago by
Michael Love
43k • written 3.8 years ago by
ahmesalama
• 0
0
votes
1
reply
1.0k
views
Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData
limma
RNASeq
RNASeqR
updated 3.7 years ago by
Gordon Smyth
52k • written 3.7 years ago by
Rita
• 0
27 results • Page
1 of 1
Recent ...
Replies
Comment: Feature Counts - potential bug with outfile.jcounts
by
chris2.a.white
• 0
Hi @yangliao, thanks for the note. We use Feature Counts extensively for gene-level counting (exon features). Unfortunately though, and I…
Comment: Feature Counts - potential bug with outfile.jcounts
by
Yang Liao
▴ 450
When you use `featureCounts` to count junctions with the `-J` option, it doesn't check if the junction is exactly overlap with exons of gen…
Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe
by
ATpoint
★ 4.6k
I think you run into the common pitfall that you treat results as categorical (significant, not significant) whereas in reality the results…
Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe
by
swbarnes2
★ 1.4k
It would probably help if you broke out the raw and normalized read counts for all the samples.
Comment: RSubread output significantly different from bash Subread output
by
Aimee
• 0
Hi Gordon, Thank you so much for this response. I went back and checked, and you are absolutely correct that it was shown in the settings b…
Votes
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: Running multiple KNN queries in parallel
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