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lindsayrutter / bigPint

Bioconductor package that makes BIG data pint-sized.
https://lindsayrutter.github.io/bigPint/
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bigPint with DESeq2 #5

Closed yeroslaviz closed 4 years ago

yeroslaviz commented 4 years ago

Hi, very good package and very clear vignettes, but can you please add some examples with DESeq2? Or at least let people know what columns are needed with a DESeq2-objects to create the plots.

thanks

lindsayrutter commented 4 years ago

Hello @yeroslaviz

Thank you for these suggestions.

1) I added a paragraph with recommendations on three columns that can ideally be used for the data metrics. These three column names are not required and can be modified manually with input parameters when creating each plot. However, creating these three columns in the data metrics object from the start is the easiest to then explore many types of plots quickly. You can see the updated paragraph with recommendations here.

2) I added reproducible code examples for creating the data metrics object using DESeq2 for data with two groups and for data with three groups. Keep in mind these are just examples using the minimum default pipelines in DESeq2. Depending on your dataset and how it aligns with suggestions in the DESeq2 vignette, you might run additional steps/normalizations in DESeq2 (or even run DESeq2 first with its simple default pipeline and then with additional steps/normalizations and compare the results visually with bigPint).

Thanks again.