[BioC] Limma: NaNs in intraspotCorrelation()

[Gordon K Smyth]

Your design, as you've set it up, has insufficient replication to do the 
statistical analysis.

A small number of warnings are not a problem, same as for 
duplicateCorrelation().

Best wishes
Gordon

On Fri, 29 Aug 2008, Muller, Pie wrote:

> Dear Gordon and Bioconductor list members,
>
> I am using limma to analyse an unlinked two-colour array experiment 
> consisting of 31 arrays (with 34,992 spots on each array) and 38 unique 
> targets. I would like to separate the two channels to perform a separate 
> channel analysis using the function lmscFit() and tried to follow the 
> example given in the limma user's guide (see below) but found that the 
> "intraspotCorrelation()" gives me nothing but NaNs. What could have gone 
> wrong? There are no NaNs in either the M or A values in my MAlist 
> object. I suspect there might something wrong with my design matrix as I 
> noticed that by reducing the design matrix to one single factor such as 
> "design=matrix(rep(1,62), ncol=1)" I receive a consensus correlation 
> value back. However, there is still another warning message "reml: Max 
> iterations exceeded in: remlscore(y, X, Z)". Does anyone have 
> suggestions as to solve this problem?
>
> In advance, many thanks for your support!
>
> Pie
>
>
> My target file:
>
>> targets
>                     Array     Cy3     Cy5
> 1  2007-06-07_B2162-09.gpr F.168.C  F.72.B
> 2  2007-06-07_B2162-13.gpr  U.48.A  U.24.A
> 3  2007-06-07_B2162-16.gpr  F.24.E  U.24.C
> 4  2007-06-07_B2162-20.gpr   F.8.C   U.8.C
> 5  2007-06-07_B2162-22.gpr  U.24.A   U.8.A
> 6  2007-06-15_B2162-02.gpr  F.48.B  F.24.D
> 7  2007-06-15_B2162-04.gpr  U.72.A  U.48.A
> 8  2007-06-15_B2162-05.gpr  F.72.B  F.48.B
> 9  2007-06-15_B2162-07.gpr  F.48.C  U.24.C
> 10 2007-06-15_B2162-10.gpr F.168.C   U.8.B
> 11 2007-06-15_B2162-11.gpr U.168.A  U.72.A
> 12 2007-06-15_B2162-19.gpr   F.8.A U.168.A
> 13 2007-06-15_B2162-23.gpr  F.72.C  U.72.C
> 14 2007-06-15_B2162-25.gpr  F.24.D   F.8.B
> 15 2007-06-15_B2162-26.gpr F.168.D U.168.C
> 16 2007-09-26_B2165-05.gpr  I.72.A  I.48.A
> 17 2007-09-26_B2165-08.gpr  I.24.A   I.8.A
> 18 2007-09-26_B2165-12.gpr   I.8.A F.168.B
> 19 2007-09-26_B2165-15.gpr   I.8.A I.168.B
> 20 2007-09-26_B2165-18.gpr I.168.A  I.72.A
> 21 2007-09-26_B2165-22.gpr  I.48.A  I.24.A
> 22 2007-09-28_B2165-02.gpr U.168.C I.168.C
> 23 2007-09-28_B2165-03.gpr I.168.C F.168.C
> 24 2007-09-28_B2165-04.gpr  I.24.B  F.24.D
> 25 2007-09-28_B2165-11.gpr  I.72.B  F.72.B
> 26 2007-09-28_B2165-14.gpr   U.8.C   I.8.C
> 27 2007-09-28_B2165-17.gpr  U.72.C  I.72.C
> 28 2007-09-28_B2165-19.gpr  I.48.B  F.48.B
> 29 2007-09-28_B2165-20.gpr  U.48.C  I.48.C
> 30 2007-09-28_B2165-23.gpr   I.8.B   F.8.B
> 31 2007-09-28_B2165-26.gpr  U.24.C  I.24.C
>
>
> My code to generate the design matrix for single channel analysis:
>
> # seperate channels
> targets.sc=targetsA2C(targets)
> u=unique(targets.sc$Target)
> f=factor(targets.sc$Target, levels=u)
> design=model.matrix(~0+f)
> colnames(design)=u
>
>
> The warnings produced by corfit=intraspotCorrelation(MA, design)
>
> ...
> Warning message:
> NaNs produced in: log(x)
> Warning message:
> NaNs produced in: log(x)
> Warning message:
> NaNs produced in: log(x)
> Warning message:
> NaNs produced in: log(x)
>
>> corfit$consensus
> [1] NaN
>
>
> The warning produced if the design matrix is reduced to one single factor:
>
>> design=matrix(rep(1,62), ncol=1)
>> corfit=intraspotCorrelation(MA, design)
> Warning message:
> reml: Max iterations exceeded in: remlscore(y, X, Z)
>
> -------------------------------------
>
> Dr Pie Müller
> Vector Group
> Liverpool School of Tropical Medicine
> Pembroke Place
> Liverpool
> L3 5QA
> UK
>
> Tel +44(0) 151 705 3225
> Fax +44(0) 151 705 3369
>
> http://www.liv.ac.uk/lstm
> http://www.ivcc.com
>