[R] Why SAM has totally diffent results in R2.1.1 and R2.4.0

[Martin Morgan]

Wei Zhao

This is not my software package and I do not use it regularly, but the
following might help in getting help from others:

* Direct any follow-up to the bioconductor mailing list

* Make sure that you are using a coherent set of current software.

* Be more precise than 'totally different'.

* Clearly indicate the software you are using.

Following my own advice, I tried

> update.packages()

to update the installed packages; I might have done

> source("http://bioconductor.org/biocLite.R")
> biocLite()

on a new installation. I then ran your suggested code (with
library(siggenes) rather than multtest), with the following output:

> library(siggenes)
Loading required package: multtest
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: survival
Loading required package: splines

Changes in siggenes:
Version 1.2.x: Added sam2excel, sam2html, and help.sam.
Version 1.5.3: Now exprSet objects can also be used in the EBAM functions
               for specifying 'data' and 'cl'.
Version 1.7.1: siggenes can also handle ExpressionSet objects.


Attaching package: 'siggenes'


        The following object(s) are masked from package:multtest :

         .mt.BLIM 

        The following object(s) are masked from package:multtest :

         .mt.naNUM 
> data(golub)
Warning message:
file 'golub.RData' has magic number 'RDA1'
   Use of save versions prior to 2 is deprecated 
> # golub.cl contains the class labels.
> golub.cl
 [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1
> # Perform a SAM analysis for the two class unpaired case assuming
> # unequal variances.
> sam.out<-sam(golub,golub.cl,B=100,rand=123)
> sam.out
SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances 
 
   Delta  p0   False Called      FDR
1    0.1 0.5 2424.77   2739  0.44276
2    0.7 0.5  262.21   1248  0.10508
3    1.3 0.5   12.11    507  0.01195
4    1.8 0.5    0.74    210  0.00176
5    2.4 0.5    0.01     76 6.58e-05
6    3.0 0.5       0     15        0
7    3.6 0.5       0      5        0
8    4.1 0.5       0      2        0
9    4.7 0.5       0      2        0
10   5.3 0.5       0      0        0

The software packages I'm using are:

> sessionInfo()
R version 2.4.0 Patched (2006-10-04 r39581) 
x86_64-unknown-linux-gnu 

locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
[7] "utils"     "datasets"  "base"     

other attached packages:
siggenes multtest survival  Biobase 
 "1.8.0" "1.11.2"   "2.29" "1.12.2" 

I found R 2.1.1 installed on a Windows laptop I have. The results of
sam.out are nearly identical (the formatting in the R 2.1.1 version
did not use scientific notation) to those presented
above. Unfortunately I do not have access to the laptop at this
instant, so cannot provide the detail above. The installed software
was, I think, siggenes 1.2.17, so not exactly comparable to
you. 

There are some suspicious items in the above, particularly the warning
about 'Use of save versions prior to 2 is deprecated' and perhaps also
the objects being 'masked'. It is hard to know whether these are worth
pursuing as a source of your problems. How does your output differ?

siggenes seems to be actively and conscientiously maintained, so a good
source for help, if the mailing list fails you, might be the package
author; try

> library(help=siggenes)

for contact information.

Hope that helps,

Martin

"wzhao" <wzhao at mednet.ucla.edu> writes:

> Hi,
>
>    I am using SAM (from siggenes_1.2.11 package) method to select genes from
> a microarray data set. After installing the latest R2.4.0 on my computer, to
> my surprise the results are totally different from that calculated using
> R2.1.1. Even the example code doesn't work the same way under these two
> versions of R. Does anybody know what is going on? Thanks for any
> suggestions.
>
>  
>
>  
>
>  library(multtest)
>  data(golub)
> # golub.cl contains the class labels.
>   golub.cl
> # Perform a SAM analysis for the two class unpaired case assuming
> # unequal variances.
>   sam.out<-sam(golub,golub.cl,B=100,rand=123)
>   sam.out
> # Obtain the Delta plots for the default set of Deltas
>   plot(sam.out)
>
>  
>
>  
>
> Best
>
> Wei Zhao
> Postdoctoral Research Fellow
> Department of Human Genetics and Biostatistics
> University of California, Los Angeles
> Gonda Neuroscience and Genetics Research Center 
> 695 Charles E. Young Drive South, Box 708822 
> Los Angeles, CA 90095-7088, USA
>
> Email: wzhao at mednet.ucla.edu
> Tel:(310)8251677
>
>
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-- 
Martin T. Morgan
Bioconductor / Computational Biology
http://bioconductor.org