[BioC] an error in normalize.quantiles {preprocessCore} function?

[697820169]

Hi all,

 I am using normalize.quantiles in package preprocessCore
to deal with my data now, and when I am trying to average
the expression value of each chip to visualize the result
of quantile normalization, I curiously found one chip seem
to have a different average expression value from others. I
have uploaded the image to imageshack:
http://img685.imageshack.us/img685/8320/mean.gif
It is noted that the average expression value of case no.184
is clearly away from other cases.

 After checking the normalized data, I have found two
cells which seemed should be 2.287524785 and 2.287870326
are replaced with both 2.28769392. I am not sure what is
causing the problem, and have tried the normalization on
two different computers, one with R 2.9.1 and preprocessCore
1.6 on a x64 system, and the other with R 2.10.1 and
preprocessCore 1.8.0 on a x86 system. However the results
are identical. My code is as follows:

library(preprocessCore)
alldata.q=as.matrix(alldata)
alldata.q=normalize.quantiles(alldata.q)
alldata.q=data.frame(alldata.q)
row.names(alldata.q)=row.names(alldata)
names(alldata.q)=names(alldata)
plot(mean(alldata.q))

And to specify which is the different spot, I have used
another code:

mean(alldata.q)==mean(alldata.q)[1]

And the result are all TRUEs, except one FALSE for case
no.184. I am not sure if there is an error in my code, or
really in the function itself.

 In order to reproduce the error to have further information, I
have uploaded the data somewhere else, since I think it unlikely
possible to attach a file as big as 31mb. Please find the file in
following url:
http://webhd.ndmctsgh.edu.tw/invite/tw/webhd/bNzQ5OS85ODkxNi8xMjcxNDExNjEw

If any further information is needed to clearify the problem, please
let me know.

kindest regards,
Tseng, Chih-hao


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