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PNNL-CompBio / beatAMLpilotProteomics

Analysis of BEAT AML patient proteomics data
MIT License
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Merge proteomics and phospho with metadata and push to synapse #5

Closed sgosline closed 3 years ago

sgosline commented 3 years ago

Here is a template for data merging: https://github.com/sgosline/p3/blob/main/dataProcessing/proteomicDataProcessing.Rmd

The table should be uploaded to the http://synapse.org/ptrc (parent id for tables will be syn22128879.

After you review metadata we can discuss on this thread.

CamiloPosso commented 3 years ago

I finally got everything installed and the data loaded. I see the metadata has "cellLine", "Ligand", "Treatment", "Time (in minutes)" and "Sample" columns, which are currently selected by the template script. The "Sensitivity" and "TMT plex" columns are omitted.

I just uploaded the merged datables (using the default selected columns from p3 template) to the syn22128879 project.

sgosline commented 3 years ago

What does "Sensitivity" represent?

CamiloPosso commented 3 years ago

I see the column lists "Sorafenib+, Gilteritinib+" and "Gilteritinib resistant". These are apparently two types chemotherapies, so I'm thinking this column has information on what kinds of therapies are most likely to affect a patient?

CamiloPosso commented 3 years ago

It seems these should be included as well, but I'm not sure my guess is correct

sgosline commented 3 years ago

Can you please point to the files in question? I'm not sure which ones we're talking about.

CamiloPosso commented 3 years ago

The script proteomicsDataProcessing (from p3) is selecting a few columns from 'syn25572050', which is a metadata table with 7 total columns.

sgosline commented 3 years ago

Update: we're waiting for @mdnestor to finish uploading the crosstabs until we finish this.