[BioC] PREDA package missing

Fri Apr 12 17:03:10 CEST 2013

Hi Maria,

I think annotations for exon arrays are organized in packages with a
different structure compared to annotation packages for other arrays.

Anyway within PREDA  there are functions to get the GenomicAnnotations
object from alternative sources in a flexible way.
I would suggest you to use the functions

GenomicAnnotationsFromdataframe
OR
GenomicAnnotationsFromfile

to get annotations for each gene (or each exon) from any data frame or
txt file. The functions parameters allow you to specify the columns
containing relevant information, such as each feature IDs etc.

Once the data are imported into a GenomicAnnotations object, you can
go on with regular analysis workflow.

All the best,
Francesco

On Fri, Apr 12, 2013 at 10:57 AM, Francesco Ferrari
<francesco.ferrari at unimore.it> wrote:
> Hi Maria,
>
> I think annotations for exon arrays are organized in packages with a
> different structure compared to annotation packages for other arrays.
>
>
> Anyway within PREDA  there are functions to get the GenomicAnnotations
> object from alternative sources in a flexible way.
> I would suggest you to use the functions
>
> GenomicAnnotationsFromdataframe
> OR
> GenomicAnnotationsFromfile
>
> to get annotations for each gene (or each exon) from any data frame or
> txt file. The functions parameters allow you to specify the columns
> containing relevant information, such as each feature IDs etc.
>
> Once the data are imported into a GenomicAnnotations object, you can
> go on with regular analysis workflow.
>
>
> All the best,
> Francesco
>
>
>
>
> On Fri, Apr 12, 2013 at 9:35 AM, Maria Arnedo Munoz
> <marnedo at staffmail.ed.ac.uk> wrote:
>> Hi everybody!
>>
>> Thanks Dan and Francesco for your advices, they worked and now I can use the
>> PREDA package.
>>
>> Now, I have another problem (sorry for asking so much questions): I am
>> analysing Human Exon arrays, because I would like to know the chromosome
>> regions with different gene expression between two cell lines, and these
>> kind of arrays are the only one that I have found for both cell lines.
>>
>> When I wrote the command:
>>
>> GEGenomicAnnotations<-eset2GenomicAnnotations(ppData, retain.chrs=1:22)
>>
>> The following message appears:
>>
>> Loading required package: pd.huex.1.0.st.v2.db
>> Warning message:
>> In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return
>> = TRUE,  :
>>   there is no package called ‘pd.huex.1.0.st.v2.db’
>> Error in mget(x, envir = getAnnMap(what, chip = data, load = load),
>> ifnotfound = NA) :
>>   error in evaluating the argument 'envir' in selecting a method for
>> function 'mget': Error: getAnnMap: pd.huex.1.0.st.v2.db package not attached
>> and load is FALSE
>>
>> I have tried to create this package (downloading the files from the
>> Affymetriz website) but I couldn't do it and a error always appears.
>>
>> Do you know if I can analyse this kind of arrays with the PREDA package? I
>> really like it, because when I trained myself with the tutorial I realize
>> that the data that I obtained are the one that I need, so any help will be
>> really really welcome.
>>
>> Sorry for the long mail,
>>
>> Thank you,
>>
>> Best
>>
>> Maria
>>
>>
>>
>>
>>
>> Quoting Francesco Ferrari <francesco.ferrari at unimore.it> on Thu, 11 Apr 2013
>> 13:16:33 -0400:
>>
>>> Hi Maria,
>>>
>>> Did you try remove.packages("PREDA") before repeating installation, as
>>> Dan suggested?
>>>
>>> It really looks a writing permission issue as Dan said.
>>> Indeed also in your R session log you can see the package is being
>>> downloaded from Bioconductor. Thus the package is available in
>>> Bioconductor repository and you are downloading it.
>>>
>>> All the best,
>>> Francesco
>>>
>>>
>>>
>>>
>>> On Thu, Apr 11, 2013 at 1:04 PM, Maria Arnedo Munoz
>>> <marnedo at staffmail.ed.ac.uk> wrote:
>>>>
>>>> Hi Dan!
>>>>
>>>> May be it is a stupid question but, how can I make you propose me? I am
>>>> the
>>>> only person that work with my computer and when I open the R program I
>>>> don't
>>>> login or something similar.
>>>>
>>>> Thanks!
>>>>
>>>> Maria
>>>>
>>>>
>>>>
>>>> Quoting Dan Tenenbaum <dtenenba at fhcrc.org> on Thu, 11 Apr 2013 09:32:55
>>>> -0700:
>>>>
>>>>> On Thu, Apr 11, 2013 at 9:16 AM, Maria [guest] <guest at bioconductor.org>
>>>>> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> Hi everybody!
>>>>>>
>>>>>> I am working with the PREDA package but today it doesn't exist in
>>>>>> anywhere. I worked with it last week and I hadn't any problem.
>>>>>>
>>>>>> I ask if it's a problem of my R program version or of the PREDA
>>>>>> package.
>>>>>>
>>>>>> I have written in the R program the following commands:
>>>>>>
>>>>>>> source("http://bioconductor.org/biocLite.R")
>>>>>>
>>>>>>
>>>>>> Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
>>>>>>
>>>>>>> biocLite("PREDA")
>>>>>>
>>>>>>
>>>>>> BioC_mirror: http://bioconductor.org
>>>>>> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
>>>>>> Installing package(s) 'PREDA'
>>>>>> trying URL
>>>>>>
>>>>>> 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/PREDA_1.4.0.zip'
>>>>>> Content type 'application/zip' length 2004077 bytes (1.9 Mb)
>>>>>> opened URL
>>>>>> downloaded 1.9 Mb
>>>>>>
>>>>>> package â€˜PREDAâ€™ successfully unpacked and MD5 sums checked
>>>>>> Warning: cannot remove prior installation of package â€˜PREDAâ€™
>>>>>>
>>>>>
>>>>> This suggests that maybe the last time the package was installed, it
>>>>> was installed by an administrator, and you (the user you are logged in
>>>>> as now) does not have permission to remove it.
>>>>>
>>>>> A solution would be to log in as an administrator and run
>>>>> remove.packages("PREDA")
>>>>> Then log back in as you and reinstall with
>>>>> source("http://bioconductor.org/biocLite.R")
>>>>> biocLite("PREDA")
>>>>>
>>>>> Dan
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> The downloaded binary packages are in
>>>>>>
>>>>>> C:\Users\marnedo\AppData\Local\Temp\RtmpaGmcOG\downloaded_packages
>>>>>>
>>>>>>> library(PREDA)
>>>>>>
>>>>>>
>>>>>> Error in library(PREDA) : there is no package called â€˜PREDAâ€™
>>>>>>
>>>>>>
>>>>>> Thanks!
>>>>>>
>>>>>> Best
>>>>>>
>>>>>> Maria
>>>>>>
>>>>>>  -- output of sessionInfo():
>>>>>>
>>>>>> R version 2.15.3 (2013-03-01)
>>>>>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>>>>>
>>>>>> locale:
>>>>>> [1] LC_COLLATE=English_United Kingdom.1252
>>>>>> [2] LC_CTYPE=English_United Kingdom.1252
>>>>>> [3] LC_MONETARY=English_United Kingdom.1252
>>>>>> [4] LC_NUMERIC=C
>>>>>> [5] LC_TIME=English_United Kingdom.1252
>>>>>>
>>>>>> attached base packages:
>>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>>>
>>>>>> other attached packages:
>>>>>> [1] BiocInstaller_1.8.3
>>>>>>
>>>>>> loaded via a namespace (and not attached):
>>>>>> [1] tools_2.15.3
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Sent via the guest posting facility at bioconductor.org.
>>>>>>
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>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> The University of Edinburgh is a charitable body, registered in
>>>> Scotland, with registration number SC005336.
>>>>
>>>>
>>>
>>>
>>
>>
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>