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Comment: Which input file is used for DGEList in EgdeR?
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Michael Love
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"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
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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…
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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
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Michael Love
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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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normawiedman059
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[103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14
[106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20
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