Entering edit mode
On Thu, Jul 16, 2009 at 5:07 AM, Manca Marco (PATH)
<m.manca@path.unimaas.nl> wrote:
>
>
> Dear Sean,
>
> good morning. I hope my email finds you well.
>
> I apologize for incomodating you with a puny question about the use
of your
> nice GEOquery packace, but I am quite a new user of it (Alberto
Goldoni, who
> is a good friend of mine and a quite active member of Bioductor
community
> whom you may know maybe) and I can not find a solution to an error
message
> which is blocking me since one whole day. I hope in your
understanding and
> support.
>
> The case is as follows:
> - I am trying to access the GSE9820 record on Gene Expression
Omnibus.
>
> - Using the command
> > gse9820<-getGEO("GSE9820", GSEMatrix=FALSE, destdir="C:\\Documents
and
> Settings\\Marco Manca\\Mijn documenten\\GSE9820")
>
> I succeeded to acquire the data (I will omitt the result of the
query
> gse9820 since it's some tens of thousands line which would just
impair our
> commnication here)
> - The command
> > Table(GSMList(gse9820)[[1]])[1:5, ]
> gives me the following output (which looks nice I think)
> ID_REF VALUE
> 1 ILMN_10000 6.88027374
> 2 ILMN_10001 12.36707372
> 3 ILMN_10002 2.41509385
> 4 ILMN_10004 6.898955513
> 5 ILMN_10005 3.728241841
>
> - But the command
> > Columns(GSMList(gse9820)[[1]])[1:5, ]
> gives me this (which looks nasty)
> Column Description
> 1 ID_REF
> 2 VALUE log2 normalized signal intensity
> NA <na> <na>
> NA.1 <na> <na>
> NA.2 <na> <na>
>
This looks this way because you asked for 5 column descriptions (1:5),
but
there are actually only two columns. Doing:
Columns(GSMList(gse9820)[[1]])
will give a prettier answer, but the data is fine, either way.
>
> - and in fact I can't manage to transform the data in an Expression
set,
> the command
> data.matrix <- log2(do.call("cbind", lapply(GSMList(gse),
function(x) {
> tab <- Table(x)
> mymatch <- match(probesets, tab$ID_REF)
> return(tab$VALUE[mymatch])
> })))
> giving me the following error message
> Error: object 'gse' not found
> Error in GSMList(gse) :
> error in evaluating the argument 'object' in selecting a method for
> function 'GSMList'
>
This is a simple cut-and-paste problem. You called your GSE "gse9820"
and
not "gse".
>
> I am sure this is due to my short experience with your package but I
can
> not find a solution (neither in my mind nor in the previous thread
in the
> mailing list) alone and I am desperately stuck at this point. Could
you give
> me any hint? Even just a suggestion of something to read to become
able to
> find a solution my self would be a much apreciated help, if not a
straight
> answer.
>
The more straightforward way of doing all this is to simply use the
GEOquery
default (at least for any newer version of GEOquery):
gse9820 <- getGEO('GSE9820')
This will return a __LIST__ of ExpressionSets and parses only the GSE
Series
Matrix file (so it is much faster than using GSEMatrix=FALSE).
Typically,
there is only one member in that list (and that is the case for
GSE9820, so
to get a single ExpressionSet, do the following:
gse9820eSet <- gse9820[[1]]
Hope that helps.
Sean
>
> Thank you in advance for your attention and support. My best
regards,
> Marco
>
>
>
> --
>
> Marco Manca, MD
>
> University of Maastricht
> Faculty of Health, Medicine and Life Science (FHML)
> Cardiovascular Research Institute Maastricht (CARIM)
> E-mail: m.manca@path.unimaas.nl
>
> "Alma Mater Studiorum" University of Bologna
> <<gc descovich="">> Atherosclerosis and Metabolic Diseases Study Centre
> Dept. of Clinical Medicine and Applied Biotechnology
> E-mail: m.manca@unibo.it
> Website: http://spazioinwind.libero.it/marco_manca_1979
>
> General Secretary of the International Society for Mathematical
Models in
> Medicine
> E-mail: medmath0@yahoo.it
>
> General Secretary of the Grupo Luso-Italiano de Arteriosclerose
> E-mail: glia.secretary@gmail.com
> Website: http://digilander.libero.it/Grupo_Luso_Italiano/
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