[BioC] quality data check

[Sean Davis]

On May 12, 2005, at 3:53 PM, Marcelo Luiz de Laia wrote:

> Dear All,
>
> We work with cDNA in nylon membranes. We use bioconductor to analyze 
> our data, basically, the packages limma, affy and vsn. The 
> normalizations are made using normalize.quantiles from affy package.
>

Normalize.quantiles does not "center" the data around 0.

> 1. it has outliers. The presented amount is very much or is relatively 
> normal for this
> platform?

This isn't the way to look for outliers.  You might want to make a 
scatter plot of replicates against each other to see how closely they 
agree.

> 2. the box is above of line zero (y axis). That is normal? After 
> normalized the data, they are between position 2 and the 3 (y axis). 
> This can happen?
>

As I mentioned above, normalize.quantiles will not center the data.  
You don't mention if you are using ratios or intensities (presumably?). 
  If you are using intensities or a common-reference design, having the 
data centered around 0 is not that important.

Sean