Hi Belinda,

I know what you mean. But  I also want to include the treatment factor.

The linear model is  mRNA=miRNA+treatment+miRNA*treatment.

So I can't use simple correlation.

Jack

2012/6/22 Belinda Phipson <phipson@wehi.edu.au>

> Hi Jack
>
> I think you have misunderstood what lmFit does. lmFit takes the data
> object/matrix, call it x, and fits a user-specified design matrix to it,
> call it design. i.e.
>
> > fit <- lmFit(x,design)
>
> From your message I don't understand what format your data is in. However,
> if you have two vectors, and you wanted to calculate a correlation, you
> could just use
>
> > cor(vector1, vector2, use=complete.obs)
>
> which would take care of the missing values.
>
> Cheers,
> Belinda
>
>
>
> > Hi all,
> >
> > I have a problem to use lmFit calculated the correlation between mRNA and
> > miRNA, because my miRNA data contained "NA" values.
> >
> > So if I use :lmFit(mRNA,miRNA), I got the message "Error in qr.default(x)
> > :
> > NA/NaN/Inf in foreign function call (arg 1)".
> >
> > The original "lm" function allow to included "NA", why lmFit can't?
> >
> > Thanks,
> >
> > Jack
> >
> >       [[alternative HTML version deleted]]
> >
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