DIA analysis 2015 Cg seed continued

Today I am continuing my work in MS stats and working with the exported Skyline report. I updated the protocol to document what I have been doing to get where I am. I am in contact with Meena from MS stats, who is helping me with an error that keeps coming up in the R code. Once that is fixed, I’ll be able to analyze the data and make some figures/tables.

Updated protocol

I updated the 02-SkylineDaily-protocol.md to share how to include all the information needed in the Skyline exported report to use in MS Stats.

MS stats

I’ll make a third protocol.md for using MS stats once it’s all sorted out. Skyline-to-MSstats-format.R

I’m still stuck at the point where I’m trying to get my converted Skyline report to work with MS stats. I have successfully changed the column names, but am stuck at the dataProcess command. I have a GitHub Issue open and Emma has been giving suggestions, but recommended I join the MS Stats google group.

I joined the group and got a response from Meena Choi from the MS Stats team, and am awaiting on her next response.

In the meantime, I’m still looking through:

I’m looking forward to moving past this dataProcess error so that I can finally compare the 23C C. gigas seed with the 29C C. gigas seed.

Written on December 14, 2018