[BioC] Questions about limma

[Sean Davis]

On Apr 5, 2005, at 12:10 PM, He, Yiwen (NIH/CIT) wrote:

> Hi, I have some questions about the data that the limma package can  
> work on.
> If I have some preprocessed/normalized data of log2 ratios from 2-color
> arrays, but not the raw signal data, can I still use lmFit?

 From the help for lmFit:

------------------------------------
Usage:

       
lmFit(object,design=NULL,ndups=1,spacing=1,block=NULL,correlation=0.75,w 
eights=NULL,method="ls",...)

Arguments:

   object: object of class 'numeric', 'matrix', 'MAList', 'marrayNorm',
           'exprSet' or 'PLMset' containing log-ratios or log-values of
           expression for a series of microarrays
----------------------------------------

So you can use a matrix of log2 ratios, yes.


> A related
> question is, can limma work on a subset of the data from an array?  For
> example, after normalization, I filter out some probes/spots. If I can
> retrieve the M and A values of that subset, can I still use limma?
>

You can use any matrix as input to lmFit that you like, doing whatever  
subsetting you like prior to its use.

> Bottom line, do I always have to start with raw data while using limma?
>

Nope, but limma offers a huge variety of normalization and diagnostic  
routines that can be very helpful if you start with raw data.

> Also, are there any test data available in the package?
>

Gordon has put a HUGE amount of time and energy into making a VERY  
comprehensive user guide.  I would start by reading it.  It will walk  
you through a number of examples; the data for all of these examples  
are included with the package.  The user guide can be found in multiple  
places, including the /doc directory of the limma package directory  
and:

http://bioinf.wehi.edu.au/limma/usersguide.pdf

Hope this helps.

Sean