[BioC] limma question

[James W. MacDonald]

In my experience lmFit() never randomly adds anything including an 
intercept when you have directly specified a design matrix.

Jim



Naomi Altman wrote:
> 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]]
>> >
>> > _______________________________________________
>> > Bioconductor mailing list
>> > 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
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> 
> 
> 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
> 


-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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