[BioC] [BioC]Li.Wong expression values < 0?

[Wolfgang Huber]

Hi Guangchun

What's wrong with negative values? It may just mean that for these genes the
MM signal is higher than the PM signal, perhaps because your complex mRNA
contains transcripts that match those MM's better than the PM's. Negative
PM-MM values that are not too far from zero may also be just because of
random fluctuations.
Best regards
Wolfgang


w.huber@dkfz.de
http://www.dkfz.de/abt0840/whuber
Tel +49-6221-424709
Fax +49-6221-42524709
DKFZ, Division of Molecular Genome Analysis
69120 Heidelberg, Germany

-----Original Message-----
From: bioconductor-admin@stat.math.ethz.ch
[mailto:bioconductor-admin@stat.math.ethz.ch]On Behalf Of Song,
Guangchun
Sent: Friday, November 08, 2002 11:01 PM
To: 'Bioconductor@stat.math.ethz.ch'
Subject: [BioC] [BioC]Li.Wong expression values < 0?


Hi,

Has anyone gotten negative expression values when using li.wong
normalization by Affy?  What the negative values mean?

Here are what I did:

> mouse <- ReadAffy()
> liwong = express(mouse, bg=subtractmm, summary.stat=li.wong)
> write.exprs(liwong,file="LiWong.txt")

The min = -2358.292881, and max = 8763.940708.


Guangchun

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