[BioC] scale and quantile normalization methods in limma

[Sean Davis]

On Thu, Jun 23, 2011 at 11:04 AM, samane fazeli <samanefazeli at gmail.com> wrote:
> Hi Sean
> Many thank you for your reply. I know the theory of these methods but i
> think they carry out in limma package differently. I want to know step by
> step performance of these processes. Is it possible?

Feel free to reply back to the list.

I'm not sure what you mean.  If you are asking how to apply these to
your dataset, as I mentioned, you will benefit from reading the limma
documentation.  If you are asking what the code does and the
documentation does not answer your question in enough detail, you can
certainly download the source code to look into things more closely.

Hope that helps.
Sean


> On Thu, Jun 23, 2011 at 7:18 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>>
>> On Thu, Jun 23, 2011 at 10:30 AM, samane fazeli <samanefazeli at gmail.com>
>> wrote:
>> > Hi all
>> > I have a problem about understanding procedure of quantile and scale
>> > normalization techniques in limma package
>> > How can i observe steps of them in software? Is there any command?
>>
>> Have a look at the help for the normalizeBetweenArrays function.
>>
>> Sean
>
>
>