[BioC] regarding GCRMA normalization

[Zhijin Wu]

We are still in the process of implementing GCRMA for the gene ST 
platforms and it is not yet included in the current version.

Best,
Jean Wu

James MacDonald wrote:
> Hi Sneha,
> 
> There are going to be several problems for you. First, the getDataAffy() function expects the data to be in a certain format which is obviously being violated here. So you _could_ modify the probe_tab file to conform to that format.
> 
> However, a bigger problem is that the chip you are using is a PM-only chip. There are some background probes on the chip, but they are not MM-probes so I don't believe the underlying assumptions for the gcrma model are going to apply.
> 
> Best,
> 
> Jim
> 
> 
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
>>>> sneha patil  01/28/10 2:04 AM >>>
> hiii,
> 
> i have prepared the HuGene-1_0-st-v1.r3.cdf package...and want to preapare a
> probe package....while making the probe package i am getting this
> error.....also my probe file is the zip file.,....
> 
>> makeProbePackage("Hugene-1_0-st-v1.r3",datafile =
> gzfile("HuGene-1_0-st-v1.probe.tab",open="r"),
> + outdir = "outdir",maintainer = "me",version = "0.0.1",species =
> "Homo_sapiens",
> + check = FALSE,force = TRUE)
> Importing the data.
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
> :
>   scan() expected 'an integer', got '+'
> 
> 
> plzz help me regarding this
> 
>     [[alternative HTML version deleted]]
> 
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-- 
------------------------------------
Zhijin (Jean) Wu
Assistant Professor of Biostatistics
Brown University, Box G-S121
Providence, RI  02912

Tel: 401 863 1230
Fax: 401 863 9182
http://www.stat.brown.edu/zwu