[BioC] problem with expresso()

Laurent Gautier laurent@cbs.dtu.dk
Wed, 15 Jan 2003 01:20:35 +0100


On Tue, Jan 14, 2003 at 01:29:30PM +0100, Wolfgang Huber wrote:
> Hi,
> 
> Oliver and I discussed this offline last Friday. The reason for the
> confusion seems to be that the summary method "medianpolish" takes the
> logarithm of the data, while, for example, "avdiff" does not. However, the
> normalization and data transformation method "vsn" also implies a data
> transformation that is like the logarithm. Thus, a call like
> 
> normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods, "vsn")
> es = expresso(data,
>          pmcorrect.method = "pmonly",
>          bgcorrect.method = "none",
>          normalize.method = "vsn",
>          summary.method   = "medianpolish")
> 
> will effectively take the logarithm of the intensities TWICE. The same call
> with summary.method   = "avdiff" would, however, produce the right result.
> Not sure how to best resolve this? I could "re-exponentiate" the data
> returned by "vsn" in normalize.AffyBatch.vsn, such that the subsequent
> log-transformation done in the summary.method would produce consistent
> results.

It would appear to be the right to proceed on my side (see below).

> However, here is a question regarding the general architecture of the affy
> package: where is the right place to take the log-transformation? In the
> "normalization"? In the "summary.method"? As an extra module? (Since some
> people, including myself, may argue that log-transformation is not the only
> thing one can do with microarray data?)

This is an interesting question. Some  people may even argue for a transformation
to be done once the expression values are obtained (i.e. once the exprSet object is obtained). Here is a suggestion:
- "intermediate" processing steps must return data on the same scale than they received them
- add two paramaters to functions like "normalize", "computeExpr" : 'transfo' 
(and 'untransfo') to specify a transformation to apply before proceeding (and
the inverse of the transformation). This would let one toy with alternatives
to log transforming... (one might also think about a collection of 'transfo and
untransfo' included in the package)

Would this appear satisfactory/reasonable ?



L.


> 
> Opinions?
> 
> Best regards
> Wolfgang
> 
> Division of Molecular Genome Analysis (Poustka Lab)
> German Cancer Research Center (DKFZ)
> Im Neuenheimer Feld 580
> 69120 Heidelberg, Germany
> 
> w.huber@dkfz.de
> http://www.dkfz.de/abt0840/whuber
> Tel +49-6221-424709
> Fax +49-6221-42524709
> 
> 
> -----Original Message-----
> From: bioconductor-admin@stat.math.ethz.ch
> [mailto:bioconductor-admin@stat.math.ethz.ch]On Behalf Of Oliver
> Hartmann
> Sent: Thursday, January 09, 2003 2:47 PM
> To: bioconductor
> Subject: [BioC] problem with expresso()
> 
> 
> Dear lsit memners,
> 
> I am trying to find a way of normalzing affy chips with vsn (I found a
> data set where rma() doesn't do well together with the t-statistic and I
> was hopeing that vsn() could fix that). I used the following script:
> 
> data <- ReadAffy()
> With this, identifying differentially expressed genes works fine
> (results are very similar to rma() - see my tech report for details if
> you like).
> But there seems to be one problem: the intensities and the values \delta
> h for differential expression (equivalent to the difference between the
> log-ratios if using rma()) are both on the wrong scale. Well, as rma()
> and other methods use log-transformed data, but vsn() uses a different
> tranformation, I think using expresso() to calculat vsn-normalized
> measures seems to log- AND arcsin-transform the data. Is there a way
> around that? From the description I didn't find a way around
> log-transformation nor where exactly the log-transformation was taking
> place.
> 
> If you are interested in the comparission of the performance of rma(),
> vsn() and MAS() tested on affymetrix data with spike in genes you can
> find a tech report at http://staff-www.uni-marburg.de/~hartmann/ - but
> only very preliminary work, sorry.
> 
> Thanks a lot
> 
> 	-oliver hartmann-
> 
> --
> Oliver Hartmann, Institute of Medical Biometry and Epidemiology
> Philipps-University Marburg, Bunsenstr. 3, D-35037 Marburg
> phone +49(0)6421 28 66514, fax +49(0)6421 28 68921
> 
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