normalising Biological replicates for differential analysis
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@f4d593ce
Last seen 26 days ago

I am new to DESEQ2 and RNA quantification and analysis in R. I have been given a dataset of 60k rows (of genes) and16 columns for 4 treatment conditions comprising of 4 repeat cell sample each. I am just confused to import the data into R and hoe to normalise the biological replicates to perform differential analysis of gene expression between these conditions? ```

DESeq2 Rtudio • 119 views
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What tutorials have you read?

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This guidance to DESeq2 http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html and RNA-seq workflow: gene-level exploratory analysis and differential expression

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The vignette opens with many many pages about of all the different ways you can import data into DESeq. Which ones have you tried?

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@mikelove
Last seen 2 days ago
United States

You'll have to ask a more specific question. You already know from the workflow how to build a dds object I suppose.

Normalization is part of the process, maybe read over the DESeq2 paper as well to understand how it works.

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