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DEgenes
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RNA-seq analysis across different experiments
limma
deseq2
normalization
degenes
design and contrast matrix
written 6.7 years ago by
mrigaya.mehra
▴ 10
3
votes
6
replies
1.3k
views
Possible approach of compare/interpret RNA-Seq results with microarray gene expression describing the same phenotype
microarray
rnaseq
DEgenes
meta-analysis
limma
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
svlachavas
▴ 830
2 results • Page
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Comment: Which input file is used for DGEList in EgdeR?
by
i.atanasoai
• 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
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