24 January 2014

expression

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Thursday - Friday notes

2014-01-23

• Lab safety training

ApTranscriptome

Preliminary finished analysis

Odd pattern that of 1,870 transcripts with significant responsive expression, 98% shared among colonies. Double-checking all code to see if this can be correct.

• Lab safety training
• Helms-Cahan lab
• Steve Keller seminar in Plant Biology

2014-01-24

ApTranscriptome

Trying to figure out why each colony has such similar expression patterns…could this really be true?

In debugging script, found major error where sailfish quantification mis-matched levels. Though a problem, this shouldn’t change the shared pattern among colonies, just which transcripts show significant responsiveness.

Also trying to speed up RxN analysis by using plyr instead of a for loop. Steep learning curve.

TODO:

• cross-check results with RSEM