I would like to work viral micro array data sets for analyzing the differential expressed gene for understanding the hidden patterns, please suggest me how handle multiple data sets for a particular virus that infects different organs.
HI!
You can use TRAM software. You can find the paper attached and the link where you can download the software and the guide. You can search GEO for the expression data you are interested in and than, with TRAM you can import gene expression data in tab-delimited text format. TRAM also allows the integration of all data by decoding probe set identifiers to gene symbols via UniGene data parsing, normalizing data from multiple platforms using intra-sample and inter-sample normalization (scaled quantile normalization), creating graphical representation of gene expression profile through two ways, "Map" and "Cluster" mode, and determining the statistical significance of results. Moreover, TRAM allows to compare two biological conditions identifying critical genomic regions and genes with significant differential expressions.
Please read the paper and the guide on line and let me know if it could be useful!
http://apollo11.isto.unibo.it/software/
Article TRAM (Transcriptome Mapper): Database-driven creation and an...
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