Grace’s Notebook: Thursday, December 14, 2017

(1) 2015 oyster seed data

I went through some more peptides on SkylineDaily with the 2015 oyster seed data. Protocol calls for checking ~100 peptides to ensure correct peak was selected (Step 5).

(2) Crab project

I met with Steven and Pam today to discuss the overall project and next steps.

Pam brought the most recent samples. There are three samples per crab, and 6 per warm-water treatment crabs (because only 3 survived). Total of 117 crabs.

I will save 50µl of hemolymph/RNAlater mixture for Pam from each crab (117 tubes total). Then I will spin down all the samples (114×3 + 3×6 = 360 samples total), remove and save the supernatant, and place supernatant and pellet tubes in -80.

In January, we will start processing the RNA and pooling the samples to be sent off for sequencing.

Yaamini’s Notebook: Remaining Analyses Part 13

Triple-nested for loops are not fun

As I mentioned in a previous post, Steven suggested I create a table with information about the peptide vs. biomarker regressions I did. I was trying to do that using a three for loops nested within eachother.

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It did not go well.

When I was talking with Sam today, he suggested I break the nested for loops. Instead, he thought I should save all of the regression information into a new table, and then reformat that information into the table I wanted to save. That was the right idea! The code can be found in this R Script, or below.

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The table I produced can be found here.

My next steps are to (finally) quality control my data, remake pH, DO and salinity plots, make a table of important environmental variables, and do something with the growth data. Oh, and write I guess.

…can you tell I’m a bit tired of this yet?