maandag 12 mei 2014

week 2 (28 April-4 May 2014)

At the begin of this week I started to make a good summary of the publication of my chosen dataset from which I run the quality rapport with array analysis.

I also showed my quality rapport  that week together with Egon Willighagen, Bart Smeets and discuss my founded quality rapport of the array analysis. After the discussion it could be concluded that we better could delete one of the baseline subject because this one was an outliner in all the founded tables and graphs. This can also have effect on the other results (subjects). So I run the analysis again without subject B11. The quality rapport was better, but still not what we wanted.

The green dot on the botom is Baseline 11
The green one at the top is Baseline 11 
It can be seen in these MA plots that the expression of the array in Baseline 11 clearly differs from the other Baseline. As example taken Baseline 10, 12 and 13, but the rest was comparable.
Later that week Lars Eijssen took a look at the rapport and further discuss it with Egon Willighagen, Bart Smeets and some other members of the department of bioinformatics at the Maastricht University. Lars advise me to split my dataset in two different groups. Because the subjects of this research came from different countries (VS and Africa) and because they also had two different project.
In this case the first dataset would contain a group from the VS that first was the baseline group and then got infected with Malaria and became the experimental group from which the pre-symptomatic effect of Malaria where compare against the baseline.

The second group would consist only subjects from Africa from which acute malaria was compared against a group with treated malaria.

At the end of this week Lars Eijsen gave a statistical lecture which all interns could (and others) from department bioinformatics could join.

2 opmerkingen:

  1. Looking at the PCA splitting the experiments seems to make a lot of sense indeed. I am actually surprised they combined them in the first place.

    Do you have the full QC report online somewhere? Array 11 indeed seems to have some issues, but for a real judgement you need all the available information. The heat map doesn't mean so much by itself. It shows you which array differs most from the rest. But there always is one that is most different and the color scale is set to that.

  2. Thanku for your reaction

    The QC report for all groups combined:

    The QC report (experimental group vs baseline)

    The QC report for the acute vs treated group malaria patient

    I still choose to go futher with these report, because it was one of the best in case of malaria research that I could found.