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
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]]
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$VALUE[mymatch])
> > })))
> >
> > Should I log2 values from MAS5
> >
> 'VALUE'("ID_REF","VALUE","DETECTION.P.VALUE")?
> >
> > since RMA gives log2 values, I am not sure what MAS5
> value means. Could
> > someone suggest a way from here.
> >
> > thanks
> > Srini
>
>
> Hi, Srini. The output of sessionInfo() and a reproducible
> example would be
> useful. We have no idea what the "MAS5" values
> are, either, without knowing
> at what GSE you are looking. And you probably don't
> need to do any of the
> cbind, lapply, etc. if you are using a recent version of
> GEOquery. But,
> again, we can't tell what version you are using.
>
> Sean
On Fri, Nov 7, 2008 at 2:46 PM, Srinivas Iyyer
<srini_iyyer_bio@yahoo.com>wrote:
> Sorry! I forgot to do attach the required information.
>
> > sessionInfo()
> R version 2.6.1 (2007-11-26)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] tools stats graphics grDevices utils datasets
methods
> base
>
> other attached packages:
> [1] GEOquery_2.2.1 RCurl_0.8-1 Biobase_1.16.2
>
> > gse <- getGEO("GSE5364")
> > range(Table(GSMList(gse)[[1]])$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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>
[[alternative HTML version deleted]]
> since RMA gives log2 values, I am not sure what MAS5 value means.
> Could someone suggest a way from here.
Hi Srini,
One quick and dirty way to know if your values are logged or not is to
look at the range of values. Log2 values will go from 0 to 16, while
unlogged values could typically go to 65535.
As Sean said, getting more details would be needed for us to know for
sure.
Francois
