[BioC] Finding genes with significant linear regression or trend

Ana Conesa aconesa at cipf.es
Mon May 19 16:05:33 CEST 2008

Dear Daniel

You could have a look into the maSigPro package. It consider time or any 
other continuous variable as such and indentifies genes with significant 
changes their expression trend for one or more than one series.

Best regards

Ana Conesa

Daniel Brewer wrote:
> What is the best way in bioconductor to find genes that have a
> significant trend with a continuous variable e.g. concentration or time.
>   This would be using microarray data and trying to find genes that show
> a dose response or a time response.  In the simplest of cases this would
> be a linear regression.  For example I have an experiment with time
> points 24,48,72,96 and I would like to find genes who have expression
> that increases with time i.e. expression is greater in each of the time
> points.
> I have looked into trying to do this with limma but the user manual only
> seems to deal with time courses with each time being a factor rather
> than a continuous variable.

Ana Conesa, PhD
Bioinformatics and Genomics Department
Centro de Investigacio'n Pri'ncipe Felipe
Avda. Autopista Saler, 16
46012 Valencia Spain

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