Showing : rnaseqr • reset
6
votes
11
replies
4.0k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 10 weeks ago by • 0 • written 3.2 years ago by ▴ 40
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
1
reply
997
views
Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 21 months ago by 42k • written 21 months ago by • 0
0
votes
3
replies
1.3k
views
using of z score in Differentially Expression Analysis
RNASeqR
updated 21 months ago by ★ 4.1k • written 21 months ago by • 0
1
vote
1
reply
794
views
edgeR for SDE analysis
RNASeqRData edgeR RNASeqR RNASeqData
updated 2.2 years ago by 50k • written 2.2 years ago by • 0
1
vote
3
replies
1.2k
views
Error with hclust
RNASeqR #hclust #wgcna #dissimilarity #average
updated 2.5 years ago by ★ 4.1k • written 2.5 years ago by • 0
4
votes
1
reply
2.0k
views
mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 2.6 years ago by 42k • written 2.6 years ago by ▴ 10
0
votes
1
reply
850
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
929
views
Outliers on DESEq2 Results
RNASeqR DifferentialExpression DESeq2
updated 2.7 years ago by 42k • written 2.7 years ago by • 0
1
vote
10
replies
3.0k
views
Duplicate correlation with limma in before-after exposure experiment
RNASeqR
3.4 years ago • updated 3.0 years ago sofie.haglund • 0
2
votes
2
replies
1.5k
views
Need help in determing upregulated and downregulated genes
RNASeqR
3.1 years ago Rishav ▴ 20
1
vote
3
replies
1.8k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
3.1 years ago dantasezequiel1 • 0
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
1
reply
885
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
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
2
replies
842
views
Bioconductor packages for doing tRNA seq analysis
RNASeqR
updated 3.2 years ago by 50k • written 3.2 years ago by ▴ 20
1
vote
3
replies
912
views
Need help in doing network analysis using R
RNASeqR
updated 3.2 years ago by ★ 4.1k • written 3.2 years ago by ▴ 20
1
vote
2
replies
844
views
Error occured in designing a matrix
RNASeqR
updated 3.2 years ago by 50k • written 3.2 years ago by ▴ 20
1
vote
5
replies
884
views
Error when calculating DE using the classical approach in edgeR
RNASeqR
3.2 years ago Rishav ▴ 20
1
vote
2
replies
1.5k
views
I am creating contrast matrix and i am following every procedure but still i don't understand where i am getting error
RNASeqR
3.2 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
1.0k
views
Using tximport to create the input for DESeq2
RNASeqR
updated 3.2 years ago by 42k • written 3.2 years ago by • 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 65k • written 3.2 years ago by ▴ 10
0
votes
2
replies
5.4k
views
TPM data in limma/voom
voom limma DifferentialExpression edgeR
3.2 years ago RJM • 0
0
votes
1
reply
754
views
Find significant genes related to a specific disease
GeneExpression RNASeqR limma
updated 3.5 years ago by ▴ 510 • written 3.5 years ago by • 0
7
votes
6
replies
3.5k
views
WHat is the difference between DEG and TopVarGenes in DESEq2?
DESeq2 R RNASeqR
3.5 years ago ecg1g15 ▴ 20
3
votes
5
replies
2.1k
views
Volcano plot - select additional gene
EnhancedVolcano RNASeqR R volcanoplot
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by ▴ 10
27 results • Page 1 of 1
Recent ...
Replies
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 65k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 65k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 65k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat by minardsmitha ▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons by boczniak767 ▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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