[BioC] limma question

[Naomi Altman]

Isn't the problem here just that lmFit adds an intercept so that the 
X matrix is singular?

--Naomi

At 03:14 PM 2/23/2006, James W. MacDonald wrote:
>Hi Sun,
>
>Sun, Yezhou wrote:
> > Hi, there,
> >
> >
> >
> > I am using limma for some single channel microarray data. Date format
> > follows that suggested by user guide: probes in row and arrays in
> > column. Data set has no missing value and was read into R by read.table
> > function. Design matrix is as following:
> >
> >
> >
> >             P          R
> >
> > P1        1          0
> >
> > P2        1          0
> >
> > P3        1          0
> >
> > P4        1          0
> >
> > P5        1          0
> >
> > P6        1          0
> >
> > P7        1          0
> >
> > R1        0          1
> >
> > R2        0          1
> >
> > R3        0          1
> >
> > R4        0          1
> >
> > R5        0          1
> >
> > R6        0          1
> >
> >
> >
> > When I ran lmFit(data, design), I got this error:
> >
> >
> >
> >
> >>fit<-lmFit(data, design)
>
>It might help if you also showed what is in the data.frame (note that
>'data' isn't a good name - you are masking an existing function). Show
>us what you get from
>
>data[1,]
>
>There may be extra things in there that you don't intend.
>
>Best,
>
>Jim
>
>
> >
> >
> > Error in qr(x) : NA/NaN/Inf in foreign function call (arg 1)
> >
> > In addition: Warning message:
> >
> > NAs introduced by coercion
> >
> >
> >
> > Traceback gave this:
> >
> >
> >>traceback()
> >
> >
> >
> >
> > 3: qr(x)
> >
> > 2: nonEstimable(design)
> >
> > 1: lmFit(data, design)
> >
> >
> >
> > I have converted data and design to numeric matrices but they never
> > worked. Could you please what's the problem? I really don't know what's
> > going on with it. Thanks a lot!
> >
> >
> >
> > Yezhou Sun
> >
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
>--
>James W. MacDonald, M.S.
>Biostatistician
>Affymetrix and cDNA Microarray Core
>University of Michigan Cancer Center
>1500 E. Medical Center Drive
>7410 CCGC
>Ann Arbor MI 48109
>734-647-5623
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111