ddRADseq Dynabeads

ApTranscriptome

Yesterday struggled with finding that some ‘Bimodal’ transcripts did not in fact have bimodal expression. Found that the reason for this was in this code

exp_type = if(coef(lmout)['val'] > 0 & coef(lmout)['I(val^2)'] > 0) "High" else {
    if(coef(lmout)['val'] < 0 & coef(lmout)['I(val^2)'] < 0) "Low" else {
        if(coef(lmout)['val'] > 0 & coef(lmout)['I(val^2)'] < 0) "Intermediate" else {
            "convex"} # close else
        } # close else
    } # close else

For transcripts with overall high levels of expression, max expression at both “Low” and “High” temperatures were greater than twice the standard deviation of expression

if(coef(lmout)['val'] < 0 & coef(lmout)['I(val^2)'] < 0) "Low"

Fixed this by requiring that max expression at both “Low” and “High” temperatures was greater than twice the standard deviation of expression at the median temp (19.25C)

Number of transcripts with maximum expression at high, low, intermediate or both high and low (bimodal) temperatures.
	Bimodal	High	Intermediate	Low	NotExp
A22	1996	865	516	1913	290
Ar	1390	757	1508	1406	519

Correct

Number of transcripts with maximum expression at high, low, intermediate or both high and low (bimodal) temperatures.
	Bimodal	High	Intermediate	Low	NotExp
A22	353	941	516	3480	290
Ar	227	869	1508	2457	519

Reading

Archiving Reproducible Research with R and Dataverse

R package for achiving data and reports on Dataverse
looks promising…but how does it compare to FigShare??