Anders Eriksson

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Progress for week 25:

on Monday, June 22nd, 2020 1:58

DTS coding
-Added progressbar for data validation
-Updated the progress bar (see figure 1)
-Fixed bug with wrong sample size (see figure 2)
-Fixed bug with unorganized barplots (see figure 2)

Figure 1. Updated progress bar
Figure 2. Correct sample size and restructured barplot

Exp always to the right:
plotOMparams <- plotOMparams[order(plotOMparams$desc),]
plotOMparams$group <- factor(plotOMparams$group, levels=paste(unique(plotOMparams$group)))

Samplesize fix:
samplesizes.annotate(boxes, as.numeric(table(plotOMparams$desc)))

progress <- c(round(l(100/(length(xml_list)))),round(flycount(100/(totalflies))))

-Finished rescreening last Thursday. Started to evaluate the new data

Optomotor platform: Ran a few more tests to confirm that the machine was still working, it is. I also adjusted the 0 line so that it is at 0, by readjusting the “zero line” screw. Looks much better now but it is still not perfectly at 0. A difference 0.1 on the computer screen translates to 100 in the evaluation chart.

Optomotor platform:
Ran a few more tests to confirm that the 0 line is always at 0. Readjusted the “zero line” screw. Looks much better now. It is still not perfectly at 0 but a difference of 0.1 in the chart translates to 100 in the evaluation graph.

Pooling data not possible: working on a fix

on Tuesday, June 2nd, 2020 12:25
Category: R code | No Comments

Dwelling time errors, prevents code from running

on Monday, May 25th, 2020 12:28
Category: R code | No Comments

Statistical evaluation of OR


Recently I measured the optomotor response in T4/T5 flies. As expected, they did not respond to the optomotor stimulus as seen in the left chart below. However, statistical evaluation struggles to quantify this difference. It might be that this is because of the low sample size, or that we are using the wrong statistical analysis?

Results from rescreen

on Monday, May 4th, 2020 1:49

Some issues with UAS-TNT control

on Monday, April 20th, 2020 1:57

I experienced some issues with the first batch of the UAS-TNT control flies, theyh ad a very low learning curve. The second batched looked fine but the still have a slightly lower learning PI during Test1 than I want.

Motion blindness in T4/T5 using Optomotor Response

on Tuesday, March 31st, 2020 1:48
T4/T5 driver line was crossed TNT line to test for motion blindness using the optomoter response assay. While the controls respond perfectly fine to the rotating striped arena the T4/T5 flies are seemingly unaware of it. Sample size for T4/T5 flies is still a bit low. However, as this is only a trial experiment for the drosophila course I consider it successful.

Making sense of dwelling data

on Tuesday, March 24th, 2020 12:54

Mean or median?


A highly hypothetical scenario of how the distribution of dwelling times could be. Even if unrealistic, it still illustrates the problem of using median instead of mean.

Plotting the dwelling times as means

An example fly of how the dwelling times are distributed over the different periods.

Grouped analysis of dwelling times

Cumming estimation plot

Used the R package Dabestr to plot the estimation statistics. The effect size and 95% CIs are plotted a separate axes

Optomotor response works consistently with old platform

on Friday, March 20th, 2020 3:23

The old platform works a lot more consistently compared to the new one. Unless major improvements are seen I do not see any reason to update it.

Updates on optomotor response software

  • Added a timer
  • Previous version generated faulty xml files. This bug has been squashed (see image below)
  • Display window of the software now also prints which direction the striped arena turns
The highlighted red areas are the ones that caused issues. Contingency has also been added to the xml file from the optomotor response (not shown). This did not cause any errors when running the DTS analysis Rscript but I thought it looked nicer having it there.