Thursday notes

ApAdaPt

Meet with Nicole to do AmPure Bead purification of double digest…but PCR plates and tubes don’t fit the magnetic plate. Had to order 300 ul round bottom PCR plates.

ApTranscriptome

Debugged analysis and repeatable results.

50% speed improvement using ddply over for loop to identify significant transcripts.

FDR correction is too conservative. For A22, while 11,846 transcripts have uncorrected P<0.05, only 4 are significant at 5% FDR, and none for Ar.

Call:

qvalue(p = pvals)

pi0: 0.3924

Cumulative number of significant calls:

<1e-04 <0.001 <0.01 <0.025 <0.05 <0.1 <1

p-value 52 344 2845 5674 11846 17600 99811

q-value 0 0 0 3 4 1085 99811

Split the analysis into ‘low’ and ‘high’ temps as discussed yesterday, and the result is no different.

Helms-Cahan lab meeting
PBio seminar - Eric von Wettberg