Entering edit mode
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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