maandag 12 mei 2014

Week 3 (5 -11 May 2014)

At the start of this week I run the array analysis from the two different groups separately. This gave already a much better quality rapport which could be used for further analysis.

The first dataset (baseline VS experimental group) was not yet completely good. Some outliners should still be erase from the dataset.
In this NUSE the data of the baseline and the experimental group is shown. There are still lots of data which are far from the median
Even though in the NUSE plot, there is a clearly marge in the PCA1/2 (first PCA plot). ALso in PCA2/3 (second PCA plot) a marge can be seen. This all afther normalization. Still lots of outliners.
In this cluster dendogram the different group are cluster togeheter, this afther normalization. Still some outliner which we might consider to exclude.
From the second dataset (acute malaria VS treated malaria) only one subjected, treated 9, was a outliner. So also this dataset I had to run without this subject. The only disadvantage would be that there is no baseline for this group.
The hybridization controls intensities and cells were OK
In the NUSE plot still lots of outliners can be seen.
No clearly marge can be seen in the PCA plot, the ouliner might have affect on this

At the end of this week I came together with Lars and his students and we discuss our dataset, rapport and the statistical analysis. Lars would help everyone with writing a script for the statistical analyses. He wrote it in the weekend of this week and at the start of next week we will discuss the scripts.

This week I also joined the first science caffé, where a lecture about statistical analysis was given.

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