[BioC] limma question

[Sun, Yezhou]

Hi, Jim,

I tried what you suggested but it's still not working. Got same error
message:

> fit<-lmFit(d[, -1], design)
Error in qr(x) : NA/NaN/Inf in foreign function call (arg 1)
In addition: Warning message:
NAs introduced by coercion 
>

I think the problem is still in data frame but I don't know what it is.
The user guide has no detailed description for single channel data set. 

Many thanks.

Yezhou

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Thursday, February 23, 2006 4:26 PM
To: Sun, Yezhou; BioConductor_list
Subject: Re: [BioC] limma question

Hi Yezhou,

It's what I suspected. The first column of your data.frame is 
non-numeric, which may be causing the problem. See if

lmFit(data[,-1], design)

works for you.

Also, please respond to the list as well. The list archives are 
searchable, so those who take the time to look can often get their 
questions answered by simply searching the archives.

HTH,

Jim



Sun, Yezhou wrote:
> Hi, Jim,
> 
> Thanks a lot for quick response. Attached text file has the first row
of
> data. Sorry I can't put it here because the line is too long. It's not
a
> mistake that data set has more experiments than design matrix because
I
> just showed part of design matrix. They actually match. I also changed
> the name of data frame but it didn't help.
> 
> Thank you.
> 
> Yezhou
> 
> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
> Sent: Thursday, February 23, 2006 3:14 PM
> To: Sun, Yezhou
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] limma question
> 
> 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