[BioC] GOstat implementation for UHN12K chips

[James W. MacDonald]

Hi Ashwin,

Ashwin Kumar wrote:
> Hello list,
> 
> In our lab we are trying to implement the GOstat package in microarray data
> analysis of UHN 12K chips.

What exactly is a UHN 12K chip?

> This is the model of our output file after analysis
> 
> "Row"    "Col"    "ProbeUID"    "ControlType"    "ProbeName"
> "GeneName"    "SystematicName"    "logFC"    "AveExpr"    "t"
> "P.Value"    "adj.P.Val"    "B"
> "4489"    79    25    4792    0    "UHNhscpg0007521"    "CASP9"    NA
> 2.35039516877896    6.66036864568585    6.34745569917956
> 0.00285473198138345    0.996108545606581    -4.49478792330771
> "5004"    79    60    5339    0    "UHNhscpg0007485"    "KLK2"    NA
> 2.59112634052802    6.86770306089859    6.27908218635525
> 0.00297451703773736    0.996108545606581    -4.49505386268111
> 
> I have tried differant parameters from the output file for proper analysis
> in GOstat but none of them worked, it will be very helpfull if anyone can
> suggest me the appropriate input parameters for  the package , taking into
> consideration the above model of data.

The appropriate input would be Entrez Gene IDs, but I don't see them 
here. I assume the manufacturer of this chip has some annotation file 
that includes some sort of reliable systematic ID? You can use the 
org.Hs.eg.db package (assuming these are human chips) to map to Entrez 
Gene and then can go from there.

Best,

Jim


> 
> A.Ashwin
> Department of Biotechnology
> Manipal Life Science Center
> Manipal University
> INDIA
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
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