[BioC] lmFit Error: "comparison of these types is not implemented"

[Martin Morgan]

Jose --

An error like this appeared in another recent email, I think because
of a version mismatch between R and Bioconductor packages. I suggest
you

1) update packages following the directions at

http://www.bioconductor.org/docs/install-howto.html

and

2) report back to the list. If you do not have success, then please
add the output of sessionInfo()

Martin

Gordon Smyth <smyth at wehi.EDU.AU> writes:

> Dear Jose,
>
> The error message you give does not originate from any limma 
> function. In fact, I've never seen it before at all.
>
> The problem isn't likely to be with quality of your data in the 
> ordinary sense. It's more likely that the data are not want you think 
> in some way.
>
> To start finding the problem you might:
>
> 1. Use trace() to find in which function the error is occuring
>
> 2. Check you data, e.g.
>
>       summary(subGeneIDMatrix[,c(2:3,16:17)])
>
> If you write again, please give sessionInfo() etc.
>
> Best wishes
> Gordon
>
>>Date: Mon, 29 Oct 2007 14:32:40 -0700
>>From: Jose Rodriguez <jarod07 at ucla.edu>
>>Subject: [BioC] lmFit Error: "comparison of these types is not
>>         implemented"
>>To: bioconductor at stat.math.ethz.ch
>>
>>I get the following error after executing the following command (using
>>limma package for microarray analysis):
>>
>>  > fit3< lmFit(subGeneIDMatrix[,c(2:3,16:17)],design)
>>Error in fit3 < lmFit(subGeneIDMatrix[, c(2:3, 16:17)], design) :
>>   comparison of these types is not implemented
>>
>>The columns of the matrix I refer to are log transformed expression
>>sets. The design matrix is simple:
>>  > design
>>        A      B
>>1      1       0
>>2      1       0
>>3      0       1
>>4      0       1
>>attr(,"assign")
>>[1] 1 1
>>attr(,"contrasts")
>>attr(,"contrasts")$`factor(c(1, 1, 2, 2))`
>>[1] "contr.treatment"
>>
>>These two sets of data I am trying to compare are part of a larger
>>experiment in which the error does not show up. Could the error be a bug
>>or does it have something to do with the quality of this particular data
>>subset?
>>Thanks!
>
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