[BioC] loged data or not loged previous to use normalize.quantile

Marcelo Luiz de Laia mlaia at fcav.unesp.br
Wed Apr 6 23:18:59 CEST 2005

Dear Fangxin Hong, Gordon Smyth, Kasper Hansen, Naomi Altman, Rhonda 
DeCook,   Wolfgang Huber, and others Bioconductor's  Friend.

I thank you kindly!

Yours posts is very important for me!

Since that I send the first message with this topic and received the 
first reply, I had that to take off a time to read about quantiles, vsn, 
amongst others subjects.

Although I not to have understood some theories, the messages and 
comments had forced me to study it.

Mr. Smyth wrote something that called my attention: background 
correction. Then, he found out my mistake.

Previously, I had only attention to the negative values: I had 
transformed they into "0". Then, after the transformation in log2, all 
values "0" had been transformed into "NA". Therefore, I was using 
*normalize.quantiles* in a matrix with values "NA".

After the email of Mr. Gordon, I transformed the negative values and 
zeros into half of the minimum value (backgroundCorrect method = 
minimum) in each column (each Array). I do this in OOCalc, because I was 
work with a matrix, not a RGList.

After that, I got significant values with raw data and with the log2 
data transformed, although the results to be slightly different.

Now I have other questions, but I will do it in another topic.

Thanks a lot!


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