Showing : RNASeqR • reset
6
votes
11
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4.0k
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How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 7 weeks ago by • 0 • written 3.2 years ago by ▴ 40
1
vote
10
replies
2.9k
views
Duplicate correlation with limma in before-after exposure experiment
RNASeqR
3.4 years ago • updated 3.0 years ago sofie.haglund • 0
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
3
votes
5
replies
2.1k
views
Volcano plot - select additional gene
EnhancedVolcano RNASeqR R volcanoplot
updated 3.5 years ago by ★ 3.9k • written 3.5 years ago by ▴ 10
5
votes
5
replies
2.5k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO RNASeqR Transcriptomics
updated 3.2 years ago by 65k • written 3.2 years ago by ▴ 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 ▴ 780 • written 3.1 years ago by ▴ 20
1
vote
5
replies
882
views
Error when calculating DE using the classical approach in edgeR
RNASeqR
3.1 years ago Rishav ▴ 20
3
votes
4
replies
1.4k
views
GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
3.1 years ago hgalmoore • 0
0
votes
3
replies
1.3k
views
using of z score in Differentially Expression Analysis
RNASeqR
updated 20 months ago by ★ 4.1k • written 20 months ago by • 0
1
vote
3
replies
1.2k
views
Error with hclust
RNASeqR #hclust #wgcna #dissimilarity #average
updated 2.4 years ago by ★ 4.1k • written 2.4 years ago by • 0
1
vote
3
replies
897
views
Need help in doing network analysis using R
RNASeqR
updated 3.1 years ago by ★ 4.1k • written 3.1 years ago by ▴ 20
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 • 0 • written 2.1 years ago by • 0
0
votes
2
replies
5.3k
views
TPM data in limma/voom
voom limma DifferentialExpression edgeR
3.2 years ago RJM • 0
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
837
views
Error occured in designing a matrix
RNASeqR
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 20
1
vote
2
replies
835
views
Bioconductor packages for doing tRNA seq analysis
RNASeqR
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 20
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
2.3k
views
Biological replicates in DESeq2
DESeq2 Bioconductor RNASeqR
updated 3.2 years ago by ★ 4.1k • written 3.2 years ago by • 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 65k • written 2.6 years ago by ▴ 20
0
votes
1
reply
919
views
Outliers on DESEq2 Results
RNASeqR DifferentialExpression DESeq2
updated 2.6 years ago by 41k • written 2.6 years ago by • 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 41k • written 2.5 years ago by ▴ 10
0
votes
1
reply
747
views
Find significant genes related to a specific disease
GeneExpression RNASeqR limma
updated 3.4 years ago by ▴ 510 • written 3.4 years ago by • 0
1
vote
1
reply
786
views
edgeR for SDE analysis
RNASeqRData edgeR RNASeqR RNASeqData
updated 2.2 years ago by 50k • written 2.2 years ago by • 0
0
votes
1
reply
967
views
Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 20 months ago by 41k • written 20 months ago by • 0
0
votes
1
reply
1.0k
views
Using tximport to create the input for DESeq2
RNASeqR
updated 3.2 years ago by 41k • written 3.2 years ago by • 0
0
votes
1
reply
861
views
Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData limma RNASeq RNASeqR
updated 3.1 years ago by 50k • written 3.1 years ago by • 0
27 results • Page 1 of 1
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Replies
Comment: Timecourse RNASeq analysis by Aurora • 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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