Hi everybody,

I would like to automate my sam output files.

I'm trying to do many SAM analysis together and would like to plot the
results and export the list of sig. genes to a file. The point is I would
like to try and make it with a R Script, so that I don't need to go into it
and change the parameter every time.

my sam command is:

> samresult    <- sam(groups, cl=classes, var.equal=FALSE, B=100,
include.zero=FALSE, gene.names=gene_names, q.version=2, R.fold=0,
na.replace=FALSE, rand=123)
 and I have two thresholds I would like to look into:
1. false positives  - the first threshold is that false < 1 (here number 5
with 0.986 false)
   Delta    p0 False Called     FDR
1    8.0 0.161 1.143     79 0.00233
2    8.1 0.161 1.071     74 0.00233
3    8.2 0.161 1.029     71 0.00233
4    8.3 0.161 1.000     69 0.00233
5    8.4 0.161 0.986     68 0.00233
6    8.5 0.161 0.971     67 0.00233
7    8.6 0.161 0.914     63 0.00233
8    8.7 0.161 0.914     63 0.00233
9    8.8 0.161 0.871     61 0.00230
10   8.9 0.161 0.829     58 0.00230
11   9.0 0.161 0.814     57 0.00230
12   9.1 0.161 0.800     56 0.00230
13   9.2 0.161 0.771     54 0.00230
14   9.3 0.161 0.771     54 0.00230
15   9.4 0.161 0.743     52 0.00230
16   9.5 0.161 0.729     51 0.00230
17   9.6 0.161 0.671     47 0.00230
18   9.7 0.161 0.657     46 0.00230
19   9.8 0.161 0.643     45 0.00230
20   9.9 0.161 0.629     44 0.00230
21  10.0 0.161 0.557     39 0.00230

The second parameter will probably be the FDR. But I still didn't find the
right %FDR to suit to my analysis.

the output I'm using till now is:
> print(samresult1h, seq(8,10,0.1))
> plot(samresult1h, 8.4)

But as you can imagine it is a tedious work to do it for many files.

My question is - Is there a possibility to tell R that I want to look only
for the first delta value where False is smaller than 1 or the FDR value has
reached a certain %?


THX for any help

Assa

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