Dear Sean,

Thanks very much for answering my question.
.
1. Can GEOquery be used with DNA methylation data in view of the fact that
the data itself is not just a summarised beta-value, but also includes the
p-value of detection above background, and the values in the U and M
channels. Will I be able to access the U, M and p-values from GEOquery?
.
2. As a novice, I'm interested in using the tools in Methylumi to perform
quality control/normalization rather than writing my own script to do this
from the start etc. Hence is there any way to do this after I have imported
the data into R?
.
3. I was told to import data by gse <- getGEO("GSExxxx")
.
then get the actual data via
data.m <- exprs(gse[[1]]),
.
and the sample information via
clin.m <- as.matrix(pData(gse[[1]])
.
and the platform annotation matrix via
anno.m <- as.matrix(Table(gpl))
.
Do I just type in "clin.m<- as.matrix(pData(gse[[1])"? When I type that in,
I get a + sign below that. What else do I need to type in?
.
Sorry for such a stupid question.
I tried looking elsewhere but could not find the answer.
.
ENS


On Sat, Oct 9, 2010 at 10:14 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:

>
>
>   On Sat, Oct 9, 2010 at 10:03 AM, S T <elengss@gmail.com> wrote:
>
>> Dear all,
>> .
>> Sorry, I am a novice user of Bioconductor.
>> I saw that Methylumi can take either Final Report format or tab delimited
>> formats.
>> May I ask whether Methylumi can import Infinium methylation data from GEO
>> -
>> specifically GSE type files?
>>
>
> It cannot.  However, once the data are loaded with getGEO(), you already
> have them in R, so there is not a need to use methylumi to load the data
> again.
>
> Sean
>
>

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