[BioC] how to run SAM analysis

M a r c e l benco81 at hotmail.com
Fri Sep 2 19:24:24 CEST 2005


if you want to run SAM anaylsis anyway, try the following (not sure if it 
works that way, but worth a try)

for example (RMA or gcRMA as you want, for gcRMA load the library gcRMA)

data.norm <- rma(data, normalize = TRUE, background = TRUE)

now construct the vector cl as needed by the SAM function:

cl <- c(0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1)


cl <- rep(0:1, c(3,14))

with 0 being the normal tissues and 1 the diseased ones. (use pData(data) to 
see the correct order of your data)

and then:

data.sam <- sam(data.norm, cl)

don´t forget to filter the genes with the genefilter function ( 
genefilter(data,flist) ) in the genefilter library!

please everyone send me positive or negative answers, would appreciate if my 
instructions were correct or not. thanks!


2px solid; MARGIN-RIGHT: 0px'><font 
style='FONT-SIZE:11px;FONT-FAMILY:tahoma,sans-serif'><hr color=#A0C6E5 
From:  <i>Adaikalavan Ramasamy 
&lt;ramasamy at cancer.org.uk&gt;</i><br>Reply-To:  
<i>ramasamy at cancer.org.uk</i><br>To:  <i>weinong han 
&lt;hanweinong at yahoo.com&gt;</i><br>CC:  
<i>bioconductor at stat.math.ethz.ch</i><br>Subject:  <i>Re: [BioC] how to run 
SAM analysis</i><br>Date:  <i>Thu, 01 Sep 2005 22:48:51 
+0100</i><br>&gt;Your design is seriously unbalanced and under-powered. I 
would suggest<br>&gt;you increase the sample size in the normal group. This 
holds no matter<br>&gt;what test statistics you plan on 
using.<br>&gt;<br>&gt;LIMMA would probably be better for your purposes. I 
_think_ it has been<br>&gt;shown empirically to hold for small sample 
sizes.<br>&gt;<br>&gt;Regards, Adai<br>&gt;<br>&gt;<br>&gt;<br>&gt;On Wed, 
2005-08-31 at 19:22 -0700, weinong han wrote:<br>&gt; &gt; Hi, List,<br>&gt; 
&gt;<br>&gt; &gt; I have 17 affymetrix .cel files and ran RMA analysis on 
them. Now I want to run SAM analysis(unpaired, 3 normal tissues and 14 
diseased tissues)  on the RMA data with R2.1.1.<br>&gt; &gt; I have 
installed the samr package.<br>&gt; &gt;<br>&gt; &gt; Questions: How to run 
the SAM analysis after the RMA analysis? The better, the more detailed 
explanations.<br>&gt; &gt;<br>&gt; &gt; Any advice and suggestions will be 
much appreciated.<br>&gt; &gt;<br>&gt; &gt;<br>&gt; &gt;<br>&gt; 
&gt;<br>&gt; &gt; Best Regards<br>&gt; &gt;<br>&gt; &gt; Han Weinong<br>&gt; 
&gt; hanweinong at yahoo.com<br>&gt; &gt;<br>&gt; &gt; 
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