How To Use Sam

Question

[avi4you]

i am a budding researcher doing my work in the field of avian influenza . 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

Answer 1

[Matt Shirley]

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

[avi4you]

i am thankful for your reply, yes i am talking about Function SAM (significant Analysis of Microarray) in bioconductor. but i am struck every time i want to perform analysis . thanks for the link i will read it and try . thanks

Answer 2

[QVINTVS_FABIVS_MAXIMVS]

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.

Have fun!