[BioC] Help: longitudinal data

Ana Conesa aconesa at cipf.es
Tue May 22 16:28:59 CEST 2007

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For analyzing time series you can make pair-wise comparisons between
times as provided by limma package.
An alternative method you can find in the Bioconductor maSigPro package
where the gene expression pattern is modeled an you can make queries on
this pattern (flat, up/downregulation, transitory response, etc). In
case you have an experiment with different treatments (i.e.. multiple
time series experiment) you can also use the maSigPro approach to
evaluate is the time pattern of a gene in the different conditions is
similar or not. Take a look at the maSigPro documentation for details on
the use of the package.

Ana Conesa

Narinder Singh Sahni wrote:
> Hello All,
> We are two students doing a project which involves analyzing
> time-course experiments. There are two strains of entamoeba histolytica 
> hybridised using Affy. measured at three different time points.
> We have two questions that would at-least get us started:
> 1) What are the best measures of filtering genes in time-course experiments.
> Some of the genes have been replicated.
> 2) What would be the most recommended techniques to focus on
> for such a sparse data set.
> Thanking all for their assistance.
> Aftab & Aditi
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