On Tue, May 29, 2012 at 11:45 AM, <ecsi@gmx.net> wrote:

>
>  So when you use system.file() you are specifically telling GEOquery to
>> look for a file that is in your GEOquery library directory, rather than
>> telling GEOquery the actual directory.
>>
>
> Thank you for explaining the system.file() thing, I didn't know that this
> was about the package repository. I thought it would be necessary to be
> able to access the downloaded files, but now I understand what's happening.
>
>
>  > mypath <- "C:/Users/bioinf_admin/**Desktop/"
>> > GSE19711 <- getGEO('GSE19711',destdir=**mypath)
>>
>> This will result in a list of ExpressionSets
>>
>
> The problem is, that here I work with methylation data, so have to create
> MethyLumiSets instead of ExpressionSets.
>
> My idea was to create phenodata.txt files using the data I get from
> getGEO():
>
> > GSE19711 <- getGEO(filename="mypath/**GSE19711_family.soft.gz")
>
> (Btw, I always get warnings when doing this, but it seems to work anyway:
> > warnings()
> Warning messages:
> 1: In readLines(con, n = chunksize) :
>  seek on a gzfile connection returned an internal error
> ...)
>
> And then accessing the information with some code like this for example:
>
> > Meta(GSMList(GSE19711)[[1]])$**characteristics_ch1[3]
>
> [1] "ageatrecruitment: 68"
>
>
> And extract the relevant substrings and create a data.frame with all the
> information I need (age, sex, treatment, etc.). And all this in an apply
> function for every GSE or something like this. Furthermore getting the data
> matrices from the soft files as well and finally creating MethyLumiSets out
> of the data matrices and the phenodata.txt files I created.
>
> Maybe it would be better to first create ExpressionSets and convert them
> into MethyLumiSets somehow, but I would have to manipulate the objects
> anyway, because I can't use the phenodata information as it comes from GEO
> in these cases. I need the phenodata to be the same style for all the GEO
> sets I have to analyze, so in any case I'll have to do the work to extract
> (only) the information I need for the different GEO sets.
>
> But I'm still not quite sure about the best way to create the
> MethyLumiSets efficiently ...
>
>
>From what you have described so far, an ExpressionSet will suffice.  I
don't think there is a need for a MethyLumiSet since you describe simply
getting the normalized data from the GSE.  I'd suggest going the route that
Jim outlined using GSEMatrix files and moving forward from there.  If you
can fill in details of what downstream analysis you want to do with the
data, perhaps we can be more directive on that point.

Sean

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