[BioC] Loess Normalization of Spotted Chip

[Tzulip Phang]

We are very interested in eliminating the print-tip effects for our 
single channel data.  Do you know if any group have tried to accomplish 
that on the single -channel oligo chips data?

Thank you

Tzu

Gordon K Smyth wrote:

>>Hi All,
>>
>>I am trying to perform loess normalization on spotted oligo chip data
>>which have only one channel, instead of two-channel in cDNA data.  I
>>would also like to use the print-tip normalization option.  I understand
>> I could use the loess normalization function from the "affy" package,
>>but I don't believe it takes into account the print-tip.  Does anybody
>>has experience in this issue?
>>    
>>
>
>See the normalizeBetweenArrays() function in the limma package for various
>methods.  Print-tip loess doesn't make nearly as much sense for single
>channel as for two colour data.  We use quantile normalization as the
>default for single-channel data.
>
>Gordon
>
>
>
>
>  
>

-- 
Tzu L. Phang, Ph.D.
303-315-1583
http://compbio.uchsc.edu/Hunter_lab/Phang


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