[BioC] short time-course design. Any suggestion?

[Naomi Altman]

You appear to have no replicates.  Without replication you cannot do any 
statistical analysis such as ANOVA or limma.

--Naomi

At 06:10 PM 7/19/2004 +0000, Stefano Calza wrote:
>Hi everybody.
>
>I'm looking at a small experiment with 12 chips (Affy), from 3 different 
>cell lines measured at 4 different time points (0,2 hours, 8 h, 24 h).
>
>1) mas5 expression values
>2) selected about 1500 genes (out of ~22000) using GO annotations for 
>those BP of possible interest
>3) selected genes with at least 25% Presence/Calls (I know this is quite 
>arbitrary).
>4) ANOVA using gls with Compound Symmetry correlation structure
>5) p value corrected either using p.adjust(...,"fdr") or computing Q values.
>
>I actually get few "significant" genes and mostly with low fold-change 
>(relative to time 0) and overall low expression intensities.
>Any objection about all this and/or any suggestion for improvement?
>
>Thanks in advance,
>Ste
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111