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

[Benilton Carvalho]

Hi Heidi,

Yes, the issue is with combine().

In Biobase, its generic function is defined as function(x, y, ...)

In gdata, it is defined as function(...)

As the warning says, gdata::combine masks Biobase::combine.

Before I make any change, I'll wait until I hear from the gdata and
Biobase maintainers.

b

On Thu, Jan 28, 2010 at 10:57 PM, Heidi Dvinge <heidi at ebi.ac.uk> wrote:
> 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
>>
>
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