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

[Benilton Carvalho]

you're looking at differences of the order 1e-10.

look at boxplot(alldata.q), and if you must compare the means, try:

means <- colMeans(alldata.q)
names(means) <- NULL
sapply(means, function(x) all.equal(x, means[1]))

b

On Fri, Apr 16, 2010 at 3:15 PM, 697820169
<697820169 at mail.ndmctsgh.edu.tw> wrote:
>
> 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
>
>
> --==Mailed via NDMCTSGH Webmail==--
>
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