[BioC] Re: marrayClasses algorithm
Jean Yee Hwa Yang
jean at biostat.ucsf.edu
Sat Feb 21 01:42:30 MET 2004
Hi Joyce,
> 1, I use read.marrayRaw() to read into my data into R, and found I have a lot
> of NA value, I would like to know what is the algorithm to calcualte this
> value. It is log ratio, do you also have certain kind of thresh value to cut
> off?
read.marrayRaw doesn't do any thresholding or cutoff. The M values are
calculated by
M = log(Rf - Rb / Gf- Gb)
Now if your Rb > Rf than is will generate NA values.
> 2, I use loess algorithm to normalize my data, and did correlation between
> replicates, they all have pretty good correlation, but I found that among
> different samples(not replicates), their correlation are still good, which
> does not make sense.
Are you using a common reference design? Are you calculating correlation
between log-ratios or log-intensities? You will see high correlation with
log-intensities. But for log-ratios, it will depends on the number of
your DE genes.
> 3, I use maPlot() to plot pre-normalization and post-normalization(which are
> implemented in PrintTip algorithm). I did see some changes between, but I saw
> the line yield down, but dot just yield a little bit more.
I don't quite follow your question. The loess line should look horizontal
post-normalization.
Will take a look at your data files.
Cheers
Jean
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