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

[Peter Davidsen]

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
>