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rnaseqr
•
reset
1
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10
replies
2.9k
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Duplicate correlation with limma in before-after exposure experiment
RNASeqR
3.4 years ago • updated 3.0 years ago
sofie.haglund
• 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
0
votes
2
replies
2.3k
views
Incorporating spike-ins to rna-seq analysis
Spike-in
RNASeqR
DESeq2
Normalization
rna-seq
updated 8 months ago by
manuel.fernandez
• 0 • written 2.1 years ago by
cicely.day
• 0
0
votes
2
replies
5.3k
views
TPM data in limma/voom
voom
limma
DifferentialExpression
edgeR
3.2 years ago
RJM
• 0
5
votes
5
replies
2.5k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO
RNASeqR
Transcriptomics
updated 3.2 years ago by
James W. MacDonald
65k • written 3.2 years ago by
H. Z. Amini
▴ 10
0
votes
1
reply
1.0k
views
Using tximport to create the input for DESeq2
RNASeqR
updated 3.2 years ago by
Michael Love
41k • written 3.2 years ago by
ahmesalama
• 0
6
votes
11
replies
4.0k
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 7 weeks ago by
Priya
• 0 • written 3.2 years ago by
Marina
▴ 40
0
votes
1
reply
2.3k
views
Biological replicates in DESeq2
DESeq2
Bioconductor
RNASeqR
updated 3.2 years ago by
ATpoint
★ 4.1k • written 3.2 years ago by
Blanca
• 0
1
vote
5
replies
882
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
838
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
900
views
Need help in doing network analysis using R
RNASeqR
updated 3.1 years ago by
ATpoint
★ 4.1k • written 3.1 years ago by
Rishav
▴ 20
7
votes
6
replies
3.4k
views
WHat is the difference between DEG and TopVarGenes in DESEq2?
DESeq2
R
RNASeqR
3.4 years ago
ecg1g15
▴ 20
0
votes
1
reply
747
views
Find significant genes related to a specific disease
GeneExpression
RNASeqR
limma
updated 3.4 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 3.4 years ago by
Will
• 0
0
votes
1
reply
863
views
Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData
limma
RNASeq
RNASeqR
updated 3.1 years ago by
Gordon Smyth
50k • written 3.1 years ago by
Rita
• 0
3
votes
4
replies
1.4k
views
GEO + RNA-seq. Total Newbie.
RNASeqData
RNASeq
GEO
RNASeqR
HELP
3.1 years ago
hgalmoore
• 0
1
vote
3
replies
1.2k
views
Error with hclust
RNASeqR
#hclust
#wgcna
#dissimilarity
#average
updated 2.4 years ago by
ATpoint
★ 4.1k • written 2.4 years ago by
devbhavin20
• 0
0
votes
1
reply
837
views
Question about normalizing and removing batch effects from bulk RNA-seq data from NCBI-SRA
Arabidopsis_thaliana_Data
RNASeqR
Normalization
BatchEffect
updated 2.6 years ago by
James W. MacDonald
65k • written 2.6 years ago by
bhandary.8590
▴ 20
0
votes
1
reply
919
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
4
votes
1
reply
2.0k
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
1
vote
1
reply
787
views
edgeR for SDE analysis
RNASeqRData
edgeR
RNASeqR
RNASeqData
updated 2.2 years ago by
Gordon Smyth
50k • written 2.2 years ago by
vikycairoli
• 0
2
votes
2
replies
1.5k
views
Need help in determing upregulated and downregulated genes
RNASeqR
3.0 years ago
Rishav
▴ 20
0
votes
1
reply
969
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
1
vote
2
replies
835
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
3
votes
5
replies
2.1k
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
1
vote
5
replies
1.6k
views
while designing matrix i got an error, please help me out
RNASeqR
updated 3.1 years ago by
Basti
▴ 780 • written 3.1 years ago by
Rishav
▴ 20
0
votes
3
replies
1.3k
views
using of z score in Differentially Expression Analysis
RNASeqR
updated 20 months ago by
ATpoint
★ 4.1k • written 20 months ago by
fatemehfakhari74
• 0
27 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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