April 04 2013

To-Do-List:
1. order the Expression data with 1s first and 0s second.
2. see why it is not being sorted by the order specified
3. make sure the design is correct. Currently the 0s are put first and the 1s are put second.
4. run the fit with different adjusting methods.

Details:
1. see why it is not being sorted by the order specified
The order is not what we expect because the order of patients in the infoTable.txt is not the same as the order of patients in the ExpressionMatrix. Through line by line debugging, I found out that (1:ncol(ExpressionMatrix))[analysis.table$Group==1]
gives back an array that holds all the indices in the infoTable whose Group is 1 (all ARs). This gives back:
7  9 12 13 14 17 23 27 28 29
but since the 7th patient in the info table doesnt map to the correct 7th patient in the ExpressionMatrix table, a wrong patient will be returned as the AR group.

2. order the Expression data with 1s first and 0s second.
I fixed it by using subsets. First getting the all the data from infoTable for ARs and sub-setting the expression Matrix based on that and then doing the same thing for NRs and then "cbind"ing them.
This time, I got much better results.

3. make sure the design is correct. Currently the 0s are put first and the 1s are put second.
I ran the code for two different designs.
a. 24 zeros first and 10 ones after.
This gave me 18 good peptides.
b. 10 zeros first and 24 ones after.
This gave me 23 good peptides.

The adjusted P values gotten from the bonferroni method were mostly 1.