[BioC] Loess Normalization of Spotted Chip
Tzulip Phang
tzu.phang at uchsc.edu
Mon Mar 8 19:28:12 MET 2004
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
>
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--
Tzu L. Phang, Ph.D.
303-315-1583
http://compbio.uchsc.edu/Hunter_lab/Phang
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