29 January 2014

RSEM

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# Wednesday notes

### CCThermBe

Grace observed colony for about 40 minutes - observed 35 blue (heat-shocked) and only 7 red (control) ants foraging!

### ApTranscriptome

Confirmed that RSEM and sailfish expression values are highly correlated, and that expression values are correlated between temperature levels for both colonies.

Re-run of script identifies unique set of responsive transcripts. Must have been bug in the sailfish step that caused duplication problems. Now fixed!

Updated and merged branch to use ddply instead of for loop.

### Dimensions meeting

• quadratic term seems to mostly be due to genes that are non-linearly decreasing or increasing expression
• focus on these linear patterns by splitting the data into ‘low’ and ‘high’ temperature groups
• 0 – 17.5 C
• 17.5 – 38.5C
• fit linear model with linear term only.
• two sets of genes
• increase expression with increasing temp
• increase expression with decreasing temp
• compare overall expression (intercept) between two colonies

KM report

• has data on C:N:P for ant pupae