[BioC] Changes in siggenes?

Thu Jan 7 17:12:16 CET 2010

Hello Bioconductor followers,

I'm quite new to R and Bioconductor and as a student in biomathematics and 
attending a paper of computational biology I'm asked to identify significantly 
expressed genes by a SAM analysis. We are working on the raw data set provided 
by Wang [1] at GEO [2] and try do reproduce their procedure and analysis for 
practical training.

For our first attempts we worked on one of the university's computers running 
MS Windows XP Professional 32bit with SP3 and R 2.9.2 (2009-08-24). By reading 
the help file for the sam() command we experimented a little bit and used the 
attributes "delta" and "p0" amongst others. It worked well and we were rather 
satisfied with the results.

Afterwards I installed R and Bioconductor on my own computer at home running 
openSUSE 11.2 (64bit) with kernel 2.6.31.5-0.1 and R 2.10.1 (2009-12-14) with 
additional Bioconductor packages installed directly from the repository on 
2010/01/05. I configured and compiled R by myself using gcc 4.4.1 [3] and it's 
complementary f77 [4] with no additional parameters.

I tried to run the same script we wrote in the university's computers and it 
broke with some error messages.
One of the errors was caused by the rma() command. This one could be fixed by 
my professor. It seemed that there have been some changes in the affy package. 
The fixed command (see file sam_analysis.r further down) is working on the old 
university computers as well.

But the sam() command still did not work with the parameters "delta" and "p0" 
and I got a error message saying that there are "unused parameters 'delta', 
'p0'.
Although we could find a way without using these I would like to know since 
when and why these parameters are not longer supported by sam(). I could not 
find a very detailed change log of the siggenes package except of this one 
(http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/siggenes), so I'm writing this 
email.

Cheers,
Torbjoern Klatt

PS: If this email is getting through to the list, it seems not possible to 
send PGP-signed mails. Is that right?

--- file: sam_analysis.r ---
#################################################
# R-Script
# author: Torbjoern Klatt
# subject: Bioinformatik
# project: SAM analysis 
# date created: 2010-01-05
# date edited last: 2010-01-06
#################################################

# set the working directory
setwd("/home/myself/Documents/Wissen/Uni/rac/0910_ws/Bioinformatik/Praktikum/wd")

# load required libraries
library(affy)           # for Affymetrix chips
library(siggenes)       # identifying significant genes
library(hgu133a2.db)    # to map the affy probe names to gene names
library(hopach)         # clustering

# read data about the phenotype (here dasatinib sensitivity)
cell.lines <- read.csv("sensitivity.csv",row.names=1,header=TRUE,sep=",")
pheno <- as.data.frame(cell.lines[,2],row.names=row.names(cell.lines))
names(pheno) <- c("sensitivity")

# read the cell files and assign phenotype information
wangData <- ReadAffy(phenoData=pheno)

## old version of previous line
### wangData <- ReadAffy()
### wangData at phenoData<-as(pheno, "AnnotatedDataFrame")

# background correction, generation of expression values and normalization
wangExpr <- rma(wangData)

# look at the expression data
sampleNames(wangExpr)
featureNames(wangExpr)
description(wangExpr)
pData(phenoData(wangExpr))
dim(exprs(wangExpr))
head(exprs(wangExpr))

# here one should do some more quality control, but this is omitted for now

# add the analysis here
# with a 'rand' value of '123' the p0 in the SAM analysis will be 0.5
sam.out <- sam(exprs(wangExpr), pData(phenoData(wangExpr))[,1], method=d.stat, 
B=500, rand=123)
## old version of previous line
### sam.out <- sam(exprs(wangExpr), pData(phenoData(wangExpr))[,1], 
method=d.stat, delta=seq(from=1.0 to=2.0 by=0.1), p0=0.5,B=500)
delta <- findDelta(sam.out,fdr=0.05)
genes <- list.siggenes(sam.out,delta[1,1])
--- END: file---

--- sessionInfo() on my linux machine ---
R version 2.10.1 (2009-12-14)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=de_DE.UTF-8
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] hgu133a2cdf_2.5.0   hopach_2.6.0        cluster_1.12.1
 [4] hgu133a2.db_2.3.5   org.Hs.eg.db_2.3.6  RSQLite_0.8-0
 [7] DBI_0.2-5           AnnotationDbi_1.8.1 siggenes_1.20.0
[10] multtest_2.2.0      affy_1.24.2         Biobase_2.6.1

loaded via a namespace (and not attached):
[1] affyio_1.14.0        MASS_7.3-5           preprocessCore_1.8.0
[4] survival_2.35-8      tools_2.10.1
--- END: sessionInfo() ---

--- sessionInfo() on the WinXP machine ---
R version 2.9.2 (2009-08-24) 
i386-pc-mingw32 

locale:
LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] hopach_2.6.0        cluster_1.12.0      hgu133a2.db_2.2.11 
 [4] RSQLite_0.8-0       DBI_0.2-5           AnnotationDbi_1.6.1
 [7] siggenes_1.18.0     multtest_2.2.0      affy_1.22.1        
[10] Biobase_2.4.1      

loaded via a namespace (and not attached):
[1] affyio_1.12.0        MASS_7.2-48          preprocessCore_1.6.0
[4] survival_2.35-4
--- END: sessionInfo()

--- references ---
[1] Xi-De Wang, Karen Reeves, Feng R Luo, Li-An Xu, Francis Lee, Edwin Clark, 
Fei Huang. (2007). Identification of candidate predictive and surrogate 
molecular markers for dasatinib in prostate cancer: rationale for patient 
selection and efficacy monitoring. Genome biology 8 (11) p. R255 
http://www.ncbi.nlm.nih.gov/pubmed/18047674
[2] http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9633
[3] extracted from config.log: gcc version 4.4.1 [gcc-4_4-branch revision 
150839] (SUSE Linux)
[4] extracted from config.log: GNU Fortran (SUSE Linux) 4.4.1 [gcc-4_4-branch 
revision 150839]