[BioC] GEOQuery - MAS5 normalized data

[Srinivas Iyyer]

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


Thanks
Srini


--- On Fri, 11/7/08, Sean Davis <sdavis2 at mail.nih.gov> wrote:

> From: Sean Davis <sdavis2 at mail.nih.gov>
> Subject: Re: [BioC] GEOQuery - MAS5 normalized data
> To: srini_iyyer_bio at yahoo.com
> Cc: bioconductor at 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 at 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