Showing : RNASeqR • reset
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
6
votes
11
replies
3.9k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 6 weeks ago by • 0 • written 3.2 years ago by ▴ 40
5
votes
5
replies
2.4k
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
4
votes
1
reply
1.9k
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
3
votes
5
replies
2.0k
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
3
votes
4
replies
1.3k
views
GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
3.1 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
830
views
Bioconductor packages for doing tRNA seq analysis
RNASeqR
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 20
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
1
vote
5
replies
875
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
826
views
Error occured in designing a matrix
RNASeqR
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 20
1
vote
3
replies
879
views
Need help in doing network analysis using R
RNASeqR
updated 3.1 years ago by ★ 4.0k • written 3.1 years ago by ▴ 20
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
3
replies
1.2k
views
Error with hclust
RNASeqR #hclust #wgcna #dissimilarity #average
updated 2.4 years ago by ★ 4.0k • written 2.4 years ago by • 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
778
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
948
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
3
replies
1.3k
views
using of z score in Differentially Expression Analysis
RNASeqR
updated 20 months ago by ★ 4.0k • written 20 months ago by • 0
0
votes
1
reply
826
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 65k • written 2.5 years ago by ▴ 20
0
votes
1
reply
912
views
Outliers on DESEq2 Results
RNASeqR DifferentialExpression DESeq2
updated 2.6 years ago by 41k • written 2.6 years ago by • 0
0
votes
2
replies
5.2k
views
TPM data in limma/voom
voom limma DifferentialExpression edgeR
3.2 years ago RJM • 0
0
votes
1
reply
741
views
Find significant genes related to a specific disease
GeneExpression RNASeqR limma
updated 3.4 years ago by ▴ 490 • written 3.4 years ago by • 0
0
votes
1
reply
2.3k
views
Biological replicates in DESeq2
DESeq2 Bioconductor RNASeqR
updated 3.1 years ago by ★ 4.0k • written 3.1 years ago by • 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 • 0 • written 2.0 years ago by • 0
0
votes
1
reply
856
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
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
27 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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