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

	[[alternative HTML version deleted]]