[BioC] oligo package cannot read files when gdata is loaded

[Heidi Dvinge]

Dear list,

I've just come across this somewhat unexpected clash between the oligo and
gdata packages. gdata is required for gplots, and is therefore loaded
whenever I plan on using heatmaps - basically always for microarray data.
However, once gdata in loaded the read.celfiles() functions fails.
Probably due to some issues with combine?

As such this can easily be avoided; just thought I'd report it here in
case anyone comes across the same when using oligo.

See example and sessionInfo below.

Thanks
\Heidi

> library(Biobase)

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

> library(oligo)
Loading required package: oligoClasses
Loading required package: preprocessCore
Welcome to oligo version 1.10.0
> library(pd.mogene.1.0.st.v1)
Loading required package: RSQLite
Loading required package: DBI
Warning message:
package 'pd.mogene.1.0.st.v1' was built under R version 2.10.1
> files<- list.celfiles("Data", full.name=TRUE)
> raw<- read.celfiles(files[1:3])
Platform design info loaded.
Reading in : Data/A1-1_(HuGene-1_0-st-v1)_2.CEL.gz
Reading in : Data/A1-2_(HuGene-1_0-st-v1)_2.CEL.gz
Reading in : Data/A1-3_(HuGene-1_0-st-v1)_2.CEL.gz
Warning message:
In AffyDate2Posix(datetime) :
  Returning dates/times as strings - format not recognized.
> library(gplots)
Loading required package: gtools
Loading required package: gdata

Attaching package: 'gdata'


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

         combine


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

         object.size

Loading required package: caTools
Loading required package: bitops
Loading required package: grid

Attaching package: 'gplots'


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

         lowess

> raw<- read.celfiles(files[1:3])
Platform design info loaded.
Reading in : Data/A1-1_(HuGene-1_0-st-v1)_2.CEL.gz
Reading in : Data/A1-2_(HuGene-1_0-st-v1)_2.CEL.gz
Reading in : Data/A1-3_(HuGene-1_0-st-v1)_2.CEL.gz
Error in as.data.frame.default(x[[i]], optional = TRUE) :
  cannot coerce class structure("AnnotatedDataFrame", package = "Biobase")
into a data.frame
In addition: Warning message:
In AffyDate2Posix(datetime) :
  Returning dates/times as strings - format not recognized.
> detach("package:gdata")
> raw<- read.celfiles(files[1:3])
Platform design info loaded.
Reading in : Data/A1-1_(HuGene-1_0-st-v1)_2.CEL.gz
Reading in : Data/A1-2_(HuGene-1_0-st-v1)_2.CEL.gz
Reading in : Data/A1-3_(HuGene-1_0-st-v1)_2.CEL.gz
Warning message:
In AffyDate2Posix(datetime) :
  Returning dates/times as strings - format not recognized.
> sessionInfo()
R version 2.10.0 (2009-10-26)
i386-apple-darwin8.11.1

locale:
[1] C

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

other attached packages:
 [1] gplots_2.7.3              caTools_1.10
 [3] bitops_1.0-4.1            gtools_2.6.1
 [5] pd.mogene.1.0.st.v1_3.0.0 RSQLite_0.7-3
 [7] DBI_0.2-4                 oligo_1.10.0
 [9] preprocessCore_1.8.0      oligoClasses_1.8.0
[11] Biobase_2.6.0

loaded via a namespace (and not attached):
[1] Biostrings_2.14.1 IRanges_1.4.1     affxparser_1.18.0 affyio_1.14.0
[5] gdata_2.6.1       splines_2.10.0
>