[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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