Question: How To Use Sam
gravatar for avi4you
5.6 years ago by
avi4you20 wrote:

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

ADD COMMENTlink modified 5.6 years ago by QVINTVS_FABIVS_MAXIMVS2.3k • written 5.6 years ago by avi4you20
gravatar for Matt Shirley
5.6 years ago by
Matt Shirley9.1k
Cambridge, MA
Matt Shirley9.1k wrote:

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:

ADD COMMENTlink written 5.6 years ago by Matt Shirley9.1k

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

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by avi4you20
5.6 years ago by

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!

ADD COMMENTlink written 5.6 years ago by QVINTVS_FABIVS_MAXIMVS2.3k
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