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

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGUv4rvYhZZsDwY1YRAjB9AJ4xhEoWqDPjchVpEu/YZ2qMonzy/QCglk/A 03mnbWpuJou6hO6WoOCHvIw= =K6Fk -----END PGP SIGNATURE-----