[BioC] regarding GCRMA normalization

Zhijin Wu zwu at stat.brown.edu
Thu Jan 28 20:02:21 CET 2010


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



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