[BioC] Do i need to do scaling normalization to the data i downloadform NCBI GEO?

[Arne.Muller@sanofi-aventis.com]

Hello,

You can check this by calculating the mean intensity per chip which should be 150.

	regards,

	Arne

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Xiao Shi
> Sent: Friday, August 26, 2005 9:01
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Do i need to do scaling normalization to the data i
> downloadform NCBI GEO?
> 
> 
> Hi everybody,
> Sorry,maybe this is not a bioconductor question,but someone 
> in this list may 
> know the answer.I want to re-analysis a microarray data set in GEO(
> http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1159) 
> .The data i 
> download are Intensities value from MAS5.0 as indicated on NCBI
> GEO.Thecorresponding article
> (Prognostically useful gene-expression profiles in acute 
> myeloid leukemia,PMID: 
> 15084694) described the Normalization procedures as follow:
>  
>    1. All intensity values were scaled to an average value of 150 per 
>    GeneChip according to the method of global scaling, or
> normalization, provided
>    in the Affymetrix Microarray Suite software, version 5.0 (MAS5.0). 
>    2. Since their methods reliably identify samples with an average 
>    intensity value of 30 or more but do not reliably 
> discriminate values 
>    between 0 and 30, these values were set to 30. 
>    3. Analysis 
> 
> My question,Do i need to do scaling normalization (to 150 per 
> GeneChip) to 
> the data i download form NCBI GEO?
> Thanks in advance.
> 
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