[BioC] data transformation
w.huber at dkfz-heidelberg.de
Wed Mar 17 21:15:19 MET 2004
the results of vsn are invariant under scaling, i.e. the
is the same as that of
except for an overall additive offset of the transformed values by a
value of log(1000).
Since log-ratios (strictly speaking, "generalized log-ratios") are
differences between transformed values, it makes no difference between
the two calls.
Hope this helps,
Rohit Ghai wrote:
> hello all
> I am trying to perform VSN normalization with one-color Codelink chip data.
> after normalization in vsn i start getting negative values all over the
> matrix... this makes it difficult to get fold changes for the genes. how
> can i get
> around this problem ? I think its because the raw intensity values i get
> from codelink
> are a bit low. I also multiplied the raw data matrix by a factor of 2.
> With the trasnformed
> data matrix VSN did not give any negative values, but the boxplots
> looked a little upward shifted
> as compared to the non-trasnformed data. The final gene list that I got
> (genes with a standard
> deviation of more than 2 in any experiment) was the same both with the
> raw data and with the
> transformed data.. but I want to know if its alright to do this?
> any ideas would be appreciated
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