[BioC] Lumi and Beadstudio 1.5.13

[claudio.is at libero.it]

dear all,

I recently tried to reload some old data anlysis which encompasses Illumina data from beastudio 1.5.13.

Notably a chunck of code that previously work now does not any more.
in particular:

> filenames <- "myData.txt"
> 
> r <- lumiR(filenames)
Error in `[.data.frame`(annotation, , "PROBE_SEQUENCE") : 
  undefined columns selected


looking in the man it seems that the package was updated to the new Illumina Bead Studio output.

looking in the ma I guessed to put inputAnnotation=FALSE. but still nothing.

r <- lumiR(filenames, inputAnnotation=FALSE)
Error in `[.data.frame`(annotation, , "PROBE_SEQUENCE") : 
  undefined columns selected

Now, I dont have the new software. what can I do?


> sessionInfo()
R version 2.7.2 (2008-08-25) 
x86_64-unknown-linux-gnu 

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] lumi_1.6.2           mgcv_1.4-1           affy_1.18.2         
[4] preprocessCore_1.2.1 affyio_1.8.1         Biobase_2.0.1