Grace’s Notebook: 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.

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Grace’s Notebook: Bioanalyzer Results – batch of cold, infected day 26

Today I ran the bioanalyzer on the batch of 8 samples from Day 26 (cold, infected) from Nov 21st. Results don’t look super great, and the ladder didn’t show up.

Gel

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Electropherogram

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Eukaryote_Total_RNA_Pico_2018-12-14_12-48-07.xad

Next steps: January 2019

We have ordered a new reagent (TRIzol LS Regent), and will have it by January. We’ll extract some RNA from some samples with that reagent and compare to yields and purity that we get from the Qiagen Kit.

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