[BioC] Re: normexp errors

[Gordon K Smyth]

I don't have any solution at this time.  Sorry.

Gordon

On Fri, May 20, 2005 2:29 am, M Perez said:
> Thanks Gordon for all your answers.
>
> I am afraid I have more questions, now about “normexp”
> background correction, I am trying to use "normexp"
> with Limma 1.8 and I got this error
>
>> RG <- backgroundCorrect(RG, method="normexp",
> offset=100);
> Corrected array 1
> Corrected array 2
> Error in optim(theta, m2loglik.normexp, control =
> list(trace = trace),  :
>   Function cannot be evaluated at initial parameters
>
> Note that only the two first files are corrected for
> background the third file seem to have something
> wrong, but when I try with Limma 1.96 and I got this
> new error:
>
>>RG <- backgroundCorrect(RG, method="normexp",
> offset=100);
> Corrected array 1
> Error in optim(c(beta, log(sigma), log(alpha)),
> sumloglik, gr = grsumloglik,  :
>         initial value in 'vmmin' is not finite
>
> Now just only the first file could be corrected using
> "normexp", I think this problem show up because of the
> nature of my files that they are “ScanArray” format
> files, as I read in other posts “normexp”  works most
> of the time but not on
> all data sets but I would like to know if is possible
> to do something before to try the “half” correction.
> Any idea what could be the reason of these errors?
> Thank you in advance.
> Manuel