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RNASeqRData
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reset
1
vote
4
replies
1.2k
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RNA-seq analysis between a wildtype vs a double microRNA kockout mouse brain
microRNA
gene
RNASeqRData
edgeR
geneontology
2.4 years ago
faiza
• 0
1
vote
3
replies
934
views
What should I do with RNA-Seq data to get a gene that work?
find
RNASeqRData
updated 2.4 years ago by
ATpoint
★ 4.7k • written 2.4 years ago by
yuhang
• 0
1
vote
4
replies
2.0k
views
merge TPM values for same geneID
RNASeqRData
TPM
updated 2.4 years ago by
ATpoint
★ 4.7k • written 2.4 years ago by
prashali.bansal
▴ 10
0
votes
0
replies
629
views
how to create PHENO_DATA
RNASeq
RNASeqData
RNASeqRData
2.5 years ago
marymshahi2021
• 0
0
votes
1
reply
816
views
DeSeq2 timecourse analysis
RNAseqRData
DeSeq2
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
Hannah
• 0
0
votes
17
replies
4.2k
views
results(dds) error: couldn't find results. you should first run DESeq()
RNASeqRData
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
beslinail
• 0
1
vote
1
reply
1.0k
views
edgeR for SDE analysis
RNASeqRData
edgeR
RNASeqR
RNASeqData
updated 3.0 years ago by
Gordon Smyth
52k • written 3.0 years ago by
vikycairoli
• 0
1
vote
2
replies
1.1k
views
Is 100K genes too many to run ComBat_seq on?
RNASeqRData
combat_Seq
BatchEffect
3.4 years ago • updated 3.1 years ago
zeegzaag
• 0
0
votes
1
reply
1.1k
views
Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData
limma
RNASeq
RNASeqR
updated 3.9 years ago by
Gordon Smyth
52k • written 3.9 years ago by
Rita
• 0
2
votes
2
replies
3.3k
views
How to download KEGG pathways for list of enriched genes
RNASeqRData
GO
4.0 years ago
Wuschel
▴ 10
0
votes
0
replies
955
views
display .CT files in a BioC package
RNAinteract
rnaseqGene
RNASeqRData
rnaseqcomp
4.1 years ago
Bogdan
▴ 670
4
votes
4
replies
1.4k
views
DEseq2: working with unbalanced number of sample in tumor study?
Deseq2
RNASeqRData
unbalancedsamplesize
updated 2.8 years ago by
Michael Love
43k • written 4.1 years ago by
Cihat
• 0
1
vote
5
replies
2.5k
views
How can I use bioconductor and Deseq2 in linux ubuntu 18
RiboProfiling
DESeq2
Bioconductor
RNASeqRData
updated 2.4 years ago by
Kevin Blighe
★ 4.0k • written 4.1 years ago by
Taufiq
• 0
13 results • Page
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Replies
Comment: how many significant figures are there in DESeq2 output
by
ATpoint
★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression
by
Jane
• 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga
by
Jane
• 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output
by
Matthew McCormack
▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to
by
ATpoint
★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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