[BioC] oligo package cannot read files when gdata is loaded
Benilton Carvalho
beniltoncarvalho at gmail.com
Tue Feb 2 15:15:32 CET 2010
That helps a lot Martin, thank you so much.
Just for the record, the problem can be reproduced in the following manner:
library(Biobase)
set.seed(1)
x = matrix(rnorm(100), nc=5)
y = annotatedDataFrameFrom(x, TRUE)
z1 = combine(y, y)
library(gdata)
z2 = combine(y, y)
b
On Tue, Feb 2, 2010 at 1:26 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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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>>
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>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
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>
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