[Bioc-devel] BioC 2.5: Added scanDates slot to Biobase's eSet class

[Patrick Aboyoun]

Dear Bioconductor developers,
The Biocore group has just committed a change to the BioC 2.5 code  
line (Biobase version 2.5.3) to support the use of microarray scan  
date in statistical analyses by adding a scanDates slot to Biobase's  
eSet class. This information can be retrieved and set using the new  
scanDates and scanDates<- function respectively. The scanDates slot is  
designed to hold a character vector of length = # of samples, with one  
character element for each sample. (See help(scanDates) for more  
information.)

In this first round of check-ins we have added affy support of this  
new slot to functions like ReadAffy and we will be working towards  
adding this information to other microarray platforms as well.

This change involved bumping the eSet version number from 1.1.0 to  
1.2.0 in the Biobase class definition. In order to minimize the impact  
of this change, the Biobase methods support both the current eSet  
version 1.2.0 as well as old 1.1.0 serialized objects so updateObject  
will not be required to be performed on eSet-derived objects prior to  
use in other functions. We have also tested and versioned bumped (and  
patched where needed) the following packages that create eSet-derived  
classes to minimize any package build issues: ACME, beadarray,  
beadarraySNP, cellHTS2, CGHbase, codelink, crlmm, GeneRegionScan,  
GGBase, maDB, oligoClasses, ontoTools, puma, rMAT, SNPchip, and  
spkTools.

Below is a demonstration of the new functionality. If you encounter  
any issues related to this change, please e-mail this list so the  
community can monitor the change.

- The Biocore Team


> suppressMessages(library(affy))
> example(ReadAffy)

RdAffy> if(require(affydata)){
RdAffy+      celpath <- system.file("celfiles", package="affydata")
RdAffy+      fns <- list.celfiles(path=celpath,full.names=TRUE)
RdAffy+  RdAffy+      cat("Reading files:\n",paste(fns,collapse="\n"),"\n")
RdAffy+      ##read a binary celfile
RdAffy+      abatch <- ReadAffy(filenames=fns[1])
RdAffy+      ##read a text celfile
RdAffy+      abatch <- ReadAffy(filenames=fns[2])
RdAffy+      ##read all files in that dir
RdAffy+      abatch <- ReadAffy(celfile.path=celpath)
RdAffy+ }
Loading required package: affydata
Reading files:
/Library/Frameworks/R.framework/Versions/2.10/Resources/library/affydata/celfiles/binary.cel
/Library/Frameworks/R.framework/Versions/2.10/Resources/library/affydata/celfiles/text.cel
> scanDates(abatch)
         binary.cel            text.cel
"01/23/04 14:30:57" "08/29/03 15:12:30"
> sessionInfo()
R version 2.10.0 Under development (unstable) (2009-06-12 r48755)
i386-apple-darwin9.6.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
other attached packages:
[1] affydata_1.11.6 affy_1.23.2     Biobase_2.5.3
loaded via a namespace (and not attached):
[1] affyio_1.13.3        preprocessCore_1.7.4 tools_2.10.0