[BioC] batch effect on variances

[Sean Davis]

On Tuesday 26 September 2006 13:29, Lana Schaffer wrote:
> Hi,
> This is just a case of matching profiles during something
> like a time course.  In packages like GeneSpring and Spotfile the user
> is allowed to chose a profile and then find other "genes" with matching
> profiles for varying correlations.  In this case I have pvalues that are
> significant for differential expression at short time periods and not
> significant at long time periods.  I want to get the list of genes with
> that profile.

Hi, Lana.

You might want to choose your genes not based on the p-value for a particular 
time point, but rather based on an f-statistic, of which there is only one 
per gene.  Then, do whatever type of clustering you like using those genes 
that show a high f-statistic.  I think a lot of folks would use kmeans or 
hierarchical clustering to then group genes that show a similar profile, but 
there are many ways to approach clustering.  

Sean