Hi all,
 
    I'm working on microarray and currently analyzing the microrarray data using limmaGUI. Loop design has been applied in this experiment. This is a 2X2 factorial experiment where there are control and treatment at 2 different time points, week 6 and 9. The experimental design is almost the same as the limmaGUI work example: Weaver Data set. I would like to look at the effect of time, treatment and interaction. I have tried to follow the limmaGUI help example to construct the design matrix. The target file and design matrix are as follow: (C - control, M - treated)
 
SlideNumberFileNameCy3Cy5
M6.C6tss37-normnew.gprM6C6
C6.C9tss5-new.gprC6C9
C9.M9tss9-new.gprC9M9
M9.M6tss24-normnew.gprM9M6
C6.M6tss31-normnew.gprC6M6
M6.M9tss2-normnew.gprM6M9
M9.C9tss12-normnew.gprM9C9
C9.C6tss25-normnew.gprC9C6

 
SlideNumberTreatmentTimeInteraction
M6.C6-100
C6.C9010
C9.M9101
M9.M60-1-1
C6.M6100
M6.M9011
M9.C9-10-1
C9.C60-10

 
According to the design matrix above, may I know what is the meaning of time effect? Does it look at the differential expression of Control sample at different time? How about treatment effect? Is it refer to the differential gene expression for Treated sample at week 6? For the effect of interaction, is it refer to both time and treatment refer, which is refer to M9?
 
Besides that, I can not figure out the second example of design matrix, Mt for Weaver data set in LimmaGUI help file. Is the design matrix looking at the effect of different time point for mutant sample? Mt11 and Mt21 refer to the effect of mutant at day 11 and day 21 alone? What is the logically theory behind to asign 1 or -1 to slides P21WT.P11WT for effect of Mt11 and Mt21? Does it has anything to do with the vector? Or we will subtract it with Wt at both time point in order for us to look at the effect of Mt11 and Mt21?
 
I use Lucidea Universal ScoreCard as my spike in control. Do I need to flag them out before I carry out the analysis? Although I have include a Spot Type file, LimmaGUI still read all the spots as genes. 
 
Thank you 
 
 
Warm regards,
Tee Sue Sean
Department of Cell and Molecular Biology,
Faculty of Biotechnology and Biomolecular Sciences,
University Putra Malaysia, 
43400 Serdang, Selangor, Malaysia.



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