[BioC] How to analysis the this kind of data set?

[Rhonda DeCook]

Hi Xiao,

It seems in a design such as this with Treatment and Time, there are a lot of 
ways to define 'differential expression'.  You say you're looking for 
differentially expressed genes with respect to treatment(a,b,ab).  So, does 
this mean you're not interested in any time effects(or any Treatment-by-Time 
interactions)?  Maybe you're looking for genes where the three expression 
profiles over time are parallel for the different treatments, but one of these 
profiles is 'far away' from the other two?  

Rhonda



> hi,everybody
> I have a *time course* data set about a CML cell line treated by two drugs 
> and their combination.The experiment was performed on cDNA microarray 
> platform.The green channel of all the arrays are common,the untreated 
> cell.Here follows the experiment design:
> 
> a_0hr,a_3hr,a_8hr,a_12hr,a_24hr,a_48hr,a_72hr, 
> b_3hr,b_8hr,b_12hr,b_24hr,b_48hr,b_72hr, 
> ab_3hr,ab_8hr,ab_12hr,ab_24hr,ab_48hr,ab_72hr.
> 
> A total of 19 *cDNA microarrays*.a_0hr means* *drug *a *treament *0 hours 
> vs. control. *And a_3hrs means drug a treatment 3 hours vs. control.So for 
> drug *b *and their combination *ab*(drug a and drug b added together).My 
> goal is to identify the three sets of genes,the genes differentially 
> expressed by drug a,the genes by drug b ,and their combination.
>  i am thinking about *ANOVA* ,but i am not sure whether it is correct.
> Any comments,suggestions?Any R/bioconductor packages can be used?Thanks in 
> advance
> 
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