@@ -32,7 +32,7 @@ Below a brief description with Bulk and scRNAseq workflow adopted in this work.
...
@@ -32,7 +32,7 @@ Below a brief description with Bulk and scRNAseq workflow adopted in this work.
"{input.bams} "
"{input.bams} "
</details>
</details>
5. DGE analysis with [edgeR]:
5. DGE analysis with [edgeR](https://bioconductor.org/packages/release/bioc/html/edgeR.html):
We employed a data analysis workflow that relied on edgeR DEGs identification setting custom biological variation coefficients (BCV) to 0.1-0.3 for the different 1vs1 comparisons performed (72h vs 24h – in each batch separately). Counts were normalized using TMM method and differential test was performed with exactTest function provided by the edgeR package (v3.32). Genes with an adjusted p.value (Benjiamini Hochberg FDR method) < 0.05 were considered differentially expressed.
We employed a data analysis workflow that relied on edgeR DEGs identification setting custom biological variation coefficients (BCV) to 0.1-0.3 for the different 1vs1 comparisons performed (72h vs 24h – in each batch separately). Counts were normalized using TMM method and differential test was performed with exactTest function provided by the edgeR package (v3.32). Genes with an adjusted p.value (Benjiamini Hochberg FDR method) < 0.05 were considered differentially expressed.
