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

[Martin Morgan]

On 02/02/2010 03:58 AM, Benilton Carvalho wrote:
> 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.

Hi Benilton, Heidi --

I saw the original post but it's not a reproducible example and there
wasn't any traceback() so I didn't chime in. I guess this is from one of
the three uses of combine() in oligo::getMetadata or oligo::getMetadata2
and the solution is likely for oligo to importMethodsFrom(Biobase,
combine) in its NAMESPACE. If the issue is somehow more subtle (e.g.,
oligo wanting to use both gdata and Biobase combine) then the solution
is to use Biobase::combine. A similar solution (import combine from
Biobase) is appropriate if the problem call is from a function defined
in a package different from oligo.

If the problem is in Heidi's 'user' code then the solution is for Heidi
to use Biobase::combine.

Hope that helps.

Martin

> 
> 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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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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