sir i am a budding researcher doing my work in the field of avian influenza . sir i want to check differential gene expression in case of avian inflenza infection in ducks. i have performed microarray experiment from commercial servicd provide Agielent . i want to use SAM for checking significantly Diffenetially expressed genes . i have already installed SAM & R but i m not able to perform analysis . please help me''' thanks in advance
If you could clarify your question a bit you might get more helpful answers. It took me a few minutes to realize you are talking about the siggenes package in Bioconductor that has a function
sam for conducting significance analysis of microarrays. Here is a PDF that might help: http://astor.som.jhmi.edu/~cope/talks/agilentdemo.pdf
I've worked with microarray data before and I was given a file that had the genome position and the Log R Ratio. In R I did a log2 transformation. Then you should calculate a Z score for each sample. Combine the samples and Z scores in a file (something like)
POS Samp1.Zscore Samp2.Zscore ... 1 2.3 0.4
Then in R there's a lot of packages for visualizing microarray data in heatmaps, for example.