Entering edit mode
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_TELE
PHONE=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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