Monday notes

Finished review for PLoS ONE
MolEcologist Q&A with Pleuni Pennings scheduled
Test to add R knitting functionality to lab notebook
allows evaluating R math and plots
use [knitcitations] for references instead of copy paste

http://stackoverflow.com/questions/4696128/bash-script-determine-if-file-modified

CCThermBe

Ideas for laser-trip camera here, here and here

Or maybe a simple time-delay

ApGXL

Bioanalyzer results from last week’s extractions.

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## Attaching package: 'pander'
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Nanodrop and Bioanalyzer results for different RNA extraction methods. Concentration in ng/ul. Extraction: R = RNAzol; R+Q = RNAzol + RNeasy; Q = RNeasy. Note that all Qiagen samples were first accidentally eluted in 170 ul and then re-precipitated using column into 17 ul.
Sample	Colony	Num_ants	Extraction	Nano_conc	Nano_qual	Bio_conc	RIN
RQ3-1	2012 A1	3	R	31.6	1.6	0.1	2.7
RQ1-1	2012 A1	1	R	13.9	1.7	0.7	8.8
RQ3-2	EW200	3	R	26.6	1.8	1.9	7.5
RQ1-2	EW200	1	R	16.2	1.9	1.4	7.1
RQ3-3	EW1000	3	R	60.3	1.7	7.4	9.6
RQ1-3	EW1000	1	R	21.4	1.6	5.1	9.5
RQ3-1	2012 A1	3	R+Q	18.9	2.1	7.6	5.9
RQ1-1	2012 A1	1	R+Q	0.7
RQ3-2	EW200	3	R+Q	0.7	0.9
RQ1-2	EW200	1	R+Q	5.9	0.5
RQ3-3	EW1000	3	R+Q	5.5	3	5.7	9.7
RQ1-3	EW1000	1	R+Q	1.6	1.6
Q1-1	2012 A1	1	Q	3.8	2	1.7	7.7
Q1-2	EW200	1	Q	2.1	1.6
Q1-3	EW1000	1	Q	3.5	2.3

Notes:

RNAzol only (R) extraction gives RIN adequate for DGE (> 7)
RNAzol elution in 100 ul gives about 100 ng
Nanodrop overestimates concentration by an order of magnitude
Nanodrop 260/280 not indicative of RIN (e.g RQ3-1 260/280 = 1.6 while RIN = 2.7)

Based on these extractions, use RNAzol extraction only (no RNeasy) for ApGXL samples. Elute in 25 ul to concentrate RNA for DGE.

New set of RNA extractions

3 Phytotron samples
3 lab ants

All 6 through RNAzol. Take aliquots for Bioanalyzer. Reserve 100 ng from RNAzol step for Phytotron samples and run remainig sample through RNeasy. Send 9 samples to Bioanalyzer.

ApTranscriptome

Updated code to output P-values, Q-values and coefficients for significant linear and quadratic terms for each transcripts