On Fri, Nov 7, 2008 at 2:46 PM, Srinivas Iyyer <srini_iyyer_bio@yahoo.com>wrote:

> Sorry! I forgot to do attach the required information.
>
> > sessionInfo()
> R version 2.6.1 (2007-11-26)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] GEOquery_2.2.1 RCurl_0.8-1    Biobase_1.16.2
>
> > gse <- getGEO("GSE5364")
> > range(Table(GSMList(gse)[[1]])$VALUE)
> [1]     0.835221 28509.953000
>
>
>
>
>
>       ID_REF     VALUE DETECTION.P.VALUE
> 1 200594_x_at 5312.5845       0.000244000
> 2 200595_s_at 2129.2195       0.000244000
> 3 200596_s_at  458.3951       0.001953125
> 4   200597_at  420.1598       0.014160156
> 5 200598_s_at 2457.5637       0.000244000
>

Great, Srini.  Those values are not logged, so you can log them if needed.
Also, you are using a fairly old version of R.  I would certainly upgrade as
soon as you can.  You'll get a lot of added functionality.

Sean



>
> --- On Fri, 11/7/08, Sean Davis <sdavis2@mail.nih.gov> wrote:
>
> > From: Sean Davis <sdavis2@mail.nih.gov>
> > Subject: Re: [BioC] GEOQuery - MAS5 normalized data
> > To: srini_iyyer_bio@yahoo.com
> > Cc: bioconductor@stat.math.ethz.ch
> > Date: Friday, November 7, 2008, 2:07 PM
> > On Fri, Nov 7, 2008 at 1:47 PM, Srinivas Iyyer
> > <srini_iyyer_bio@yahoo.com>wrote:
> >
> > > Dear group / Dear Sean,
> > > I am using GEOQuery to download a MAS5 (U133Plus2
> > platform) and intend to
> > > make it into a expression matrix and compute
> > differential expression between
> > > two classes of samples.
> > >
> > > I have downloaded the data into a gse object.  while
> > making a exprSet
> > > object using code in vignette:
> > > data.matrix <- log2(do.call("cbind",
> > lapply(GSMList(gse), function(x) {
> > > tab <- Table(x)
> > >  mymatch <- match(probesets, tab$ID_REF)
> > >  return(tab$VALUE[mymatch])
> > >  })))
> > >
> > > Should I log2 values from MAS5
> > >
> > 'VALUE'("ID_REF","VALUE","DETECTION.P.VALUE")?
> > >
> > > since RMA gives log2 values, I am not sure what MAS5
> > value means. Could
> > > someone suggest a way from here.
> > >
> > > thanks
> > > Srini
> >
> >
> > Hi, Srini.  The output of sessionInfo() and a reproducible
> > example would be
> > useful.  We have no idea what the "MAS5" values
> > are, either, without knowing
> > at what GSE you are looking.  And you probably don't
> > need to do any of the
> > cbind, lapply, etc. if you are using a recent version of
> > GEOquery.  But,
> > again, we can't tell what version you are using.
> >
> > Sean
>
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