As suggested by Wolfgang, I send this question to bioconductor mail list and
I would like to hear other expert's feedback the message is as below with a
bit modification:


another question:
which way you think is a better solution for normalization with using vsn,
you suggested normalize each array separately, in fact the 30 arrays form a
whole genome data set, should normalizing them as a whole data set be a
better way?

>
> I have been using vsn package of R to normalize NimbleGen's ENCODE tiling
arrays
> (383000 probes), and vsn gave us very good results. Now,We are trying data
> analysis for NimbleGen whole genome tiling arrays, which is a very large
> dataset (30 arrays,total more than  22000000 probes). I combined all of
these
> array intensity data together, and tried doing within array vsn
normalization
> for this combined large dataset. Since in fact the 30 arrays should be
consider a whole array set
 Apparently, because of the size of the data
> set, I can not run vsn packages of R (memory problem). Therefore, I am
> wondering if you have a c version vsn or any other methods to deal with
such
> huge datasets.
>
> Thank you very much.
>
> roger



which version are you using? Please consider version >= 2.0.35 (from
www.bioconductor.org), the function "vsn2" is already written in C. Also
please consult the function parameter "subsample".

I think you should normalize each array separately. I have very
successfully used vsn for tiling arrays with 6.5 Mio probes.

Also, for this type of question of general interest, please use the
bioconductor mailing list! (See link on
http://www.bioconductor.org<https://webmailapp4.cc.utexas.edu/horde-2.2.9-assign/util/go.php?url=http%3A%2F%2Fwww.bioconductor.org&Horde=0be2d1ba79b54c02c71a2cf118f20902>
)
That way you get feedback from many other experts as well, other users
also benefit, and the discussion remains searchable in the archives.

Best wishes
   Wolfgang

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