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Replace dep_results dataset #48

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csdaw opened this issue Apr 26, 2022 · 3 comments
Open

Replace dep_results dataset #48

csdaw opened this issue Apr 26, 2022 · 3 comments

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@csdaw
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csdaw commented Apr 26, 2022

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
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csdaw commented Apr 26, 2022

This one looks good PXD002032.

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

@csdaw
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csdaw commented Apr 26, 2022

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

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Fully on board 👍

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@TomSmithCGAT @csdaw