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Readme update
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KamilMaliszArdigen committed Nov 5, 2024
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Expand Up @@ -73,6 +73,10 @@ RNA-seq limma+voom:
```

:::note
If you would like to use advanced mixed models please create new column in submission sheet with . <dot> seperated values forming the composite variable.

See the [issue 325](https://github.com/nf-core/differentialabundance/issues/325) for more information.
:::note2
If you are using the outputs of the nf-core rnaseq workflow as input here you should provide either the **gene_counts_length_scaled.tsv** or **gene_counts_scaled.tsv** matrices. This follows the [recommendation from the tximport documentation](https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html#limma-voom):

> "Because limma-voom does not use the offset matrix stored in `y$offset`, we recommend using scaled counts generated from abundances, either 'scaledTPM' or 'lengthScaledTPM'."
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