[BioC] Loess Normalization of Spotted Chip

[Gordon K Smyth]

> 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