Replace `dep_results` dataset

CambridgeCentreForProteomics / camprotR

https://cambridgecentreforproteomics.github.io/camprotR/

MIT License

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Replace `dep_results` dataset #48

Open csdaw opened 2 years ago

csdaw commented 2 years ago

I use the dep_results dataset for testing the GO functions. It is based on the DEP::UbiLength dataset, which is a MaxQuant proteingroups.txt output.

I find UbiLength to not be well documented enough/biologically interpretable enough to use. I think we should just use a MaxQuant proteingroups.txt file directly from some LFQ PRIDE submission (I am looking for a suitable one now...).

csdaw commented 2 years ago

This one looks good PXD002032.

MDA-MB-231 cells (breast cancer), LFQ, n = 6, HGMA1 silenced cells (A) vs control siRNA (C)

csdaw commented 2 years ago

What do you think @TomSmithCGAT? Would also be useful for writing a GO vignette...

TomSmithCGAT commented 2 years ago

Fully on board 👍