[BioC] normalization for custom chip
huber at ebi.ac.uk
Thu Nov 18 13:52:08 CET 2004
M Inmaculada Barrasa wrote:
> Hi Wolfram,
> I read this in a previous e-mail on this thread.
>> I do not recommend using house keeping genes for normalization. In
>> several experiments they turn out being differentially expressed.
>> A better approach would be to use a normalization method that searches
>> for an invariant set of genes in the sample. "VSN" and Li & Wong's
>> "invariant set" do that. The methods have limits though regarding
>> the minimum proportion of not differentially expressed genes.
>> Below 30% things become difficult. ....
> Can you please give more details on how would you apply VSN to search for
> invariant set of genes that can be later used to normalize the array.
> Sorry if I am making so sense.
> I will read your paper carefully
vsn does not directly search for an "invariant set". Rather, it regards
the fitting of scale factors and background offsets as a parameter
estimation problem and uses a standard robust estimation technique for
this. The performance of this estimator, and in particular the
sensitivity to total number and asymmetric proportions of up- and
down-regulated genes, is discussed in (hopefully exhaustive) detail in
Parameter estimation for the calibration and variance stabilization of
microarray data. W. Huber, A. von Heydebreck, H. Sültmann, A. Poustka,
M. Vingron. Statistical Applications in Genetics and Molecular Biology
2003 Vol. 2: No. 1, Article 3
in particular, Fig. 8 shows that up to about 30% of differentially
expressed genes are OK that are all up or all down, and more, if they
are more symmetric.
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