[BioC] issue with lmFit in limma

[Sean Davis]

On Thu, Dec 11, 2008 at 6:02 PM, Skewes,Aaron <ASkewes at mdanderson.org> wrote:
> Hi,
>
> I am attempting to process a few Agilent 4x44 based arrays using limma. When I try to estimate expression levels with lmFit in limma, I get the following message:
>
> Warning message:
> In lmFit(MA, method = "robust") :
> Some coefficients not estimable: coefficient interpretation may vary.
>
> And all the coeff's are NA. I am not at all sure what the problem is? Can someone give me an idea?
>
> Code snipet:
>
> #Normalize data with background subtraction
>        MA<-normalizeWithinArrays(RG.Nctr , method="loess", bc.method="rma" )
>        MA<-normalizeBetweenArrays(MA , method="quantile")
>
>        #get exp values
>        fit <- lmFit(MA)

Hi, Aaron.  You'll need to read the limma user guide and help pages
for lmFit and any other functions that you plan to use.  To give you a
place to start, you will need to define a design matrix before lmFit
will be helpful for you.  If something in the help and user guide
isn't clear, feel free to ask for more detail.  Also, when you write
to the list, be sure to include the output of sessionInfo().

Hope that helps.

Sean