[BioC] lmFit only deals with numerical values (data matrix object)?

[Holger Schwender]

Numeric values do not necessarily need to be positive. They can also be negative. So you can use your log2 ratios as they are (no matter whether they are positive or negative).

Holger


-------- Original-Nachricht --------
> Datum: Fri, 8 Apr 2011 15:20:46 +0200
> Von: Peter Davidsen <pkdavidsen at gmail.com>
> An: Sean Davis <sdavis2 at mail.nih.gov>
> CC: bioconductor at r-project.org, bioconductor at stat.math.ethz.ch
> Betreff: Re: [BioC] lmFit only deals with numerical values (data matrix	object)?

> Hi Sean,
> 
> I read it, but wasn't 100% sure!
> 
> Okay, as microarray data need to be log-transformed in order to
> compare gene activities -
> Could I then, if I want to use the lmFit function i limma:
> 1) transform all my log2 ratio data in my data matrix into fold change
> - 2^(log2 ratio)
> 2 divide fold change by 100 => decimal numbers
> 3) add the value +1 to all decimal numbers
> 4) log2 transform all decimal numbers (=> all expression values now
> numerical)
> 
> Sorry for the obvious questions, but I'm new to chip analysis, and
> thus quite unsure
> 
> Kind regards
> 
> On 8 April 2011 13:28, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> > On Fri, Apr 8, 2011 at 7:13 AM, Peter Davidsen <pkdavidsen at gmail.com>
> wrote:
> >> Hi List
> >>
> >> Does "lmFit" in limma only deals with numeric values (positive
> numbers)?
> >> I have created a data matrix object with log2 ratio data (some data
> >> assume negative values).
> >> Can I use my data matrix as object in the lmFit function?
> >
> > Hi, Peter.
> >
> > You should read the help for lmFit, but to answer your question, yes a
> > numeric matrix can be used for lmFit.
> >
> > Sean
> >
> 
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