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 ???PREDA??? successfully unpacked and MD5 sums checked
>>>>> Warning: cannot remove prior installation of package ???PREDA???
>>>>>
>>>>
>>>> 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 ???PREDA???
>>>>>
>>>>>
>>>>> 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.
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at r-project.org
>>>>>
https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>>
http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> 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.
>
>
