[BioC] limma question

[James W. MacDonald]

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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-- 
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