[BioC] warning message for duplicateCorrelation

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Oops, I didn't see this one. By changing the subject of your original
post, you are starting a new thread and make it harder for people that
follow things by threads. I'm answering in the original thread so it will
be easier for the follow up.

What I've seen is that the duplicateCorrelation function doesn't call
directly 'sqrt(dfitted.values)' but calls the mixedModel2Fit function
(statmod package) which itself makes the call to 'sqrt(dfitted.values)'.

Now only a limma expert can tell us whether or not you can safely ignore
this message, or if you are not using duplicateCorrelation properly, or if
there is something wrong with your data, or if there is a bug in the
duplicateCorrelation function, or in the mixedModel2Fit function, etc...

H.


> Hi again!
>
> I thought it might be better to add some information to my message
> concerning my problem using the duplicateCorrelation function in Limma
> (see below).
>
> The arrays are used are printed in duplicates with a spacing of 15000 (so
> in total 30000 features per array) and I did the imageprocessing using
> GenePixPro6.1.
>
> This is what I have done before applying the dupcor-function:
>
>> targets=readTargets("Targets_basicSat.txt")
>> targets
>    SlideNumber          FileName Cy3 Cy5
> 1            1 3096_basicSat.gpr ref   A
> 2            2 3079_basicSat.gpr   A ref
> 3            3 3089_basicSat.gpr ref   A
> 4            4 3081_basicSat.gpr   A ref
> 5            5 3071_basicSat.gpr ref   B
> 6            6 3082_basicSat.gpr   B ref
> 7            7 3085_basicSat.gpr ref   B
> 8            8 8268_basicSat.gpr   B ref
> 9            9 7829_basicSat.gpr ref   C
> 10          10 3086_basicSat.gpr   C ref
> 11          11 7823_basicSat.gpr ref   C
> 12          12 7826_basicSat.gpr   C ref
> 13          13 3090_basicSat.gpr ref   D
> 14          14 3091_basicSat.gpr   D ref
> 15          15 3092_basicSat.gpr ref   D
> 16          16 7827_basicSat.gpr   D ref
>
> Every other slide is a dyeswapped technical replicate and per "group"
> (A,B,C,D) there are 2 biological replicates.
>
>> K=read.maimages(targets$FileName, source="genepix.median",
> wt.fun=wtflags(0))
>> types=readSpotTypes("SpottypesGAPDH.txt")
>> Status=controlStatus(types, K)
>> K$genes$Status=Status
>> K2=backgroundCorrect(K, method=”subtract”)
>> K2=normalizeWithinArrays(K2, method="median")
>> design=modelMatrix(targets, ref="ref")
>> design
>       A  B  C  D
>  [1,]  1  0  0  0
>  [2,] -1  0  0  0
>  [3,]  1  0  0  0
>  [4,] -1  0  0  0
>  [5,]  0  1  0  0
>  [6,]  0 -1  0  0
>  [7,]  0  1  0  0
>  [8,]  0 -1  0  0
>  [9,]  0  0  1  0
> [10,]  0  0 -1  0
> [11,]  0  0  1  0
> [12,]  0  0 -1  0
> [13,]  0  0  0  1
> [14,]  0  0  0 -1
> [15,]  0  0  0  1
> [16,]  0  0  0 -1
>
>> cor=duplicateCorrelation(K2, design=design, ndups=2, spacing=15000,
> weights=K2$weights)
>
> And at this point, I get the warning message "NaNs produced in:
> sqrt(dfitted.values)" and I do not know if I should simply procede or if
> this warning indicates a major problem.
>
> I hope somebody can help and that this is sufficient information.
> Kind regards,
> Dorthe
>
>
> Hi,
>
> when using the dulicateCorrelation function I get the following warning
> message: "NaNs produced in: sqrt(dfitted.values)"
> I have used the function before and usually got the "too much damping"
> warning message, which I know can be ignored. But now I get the warning
> message metioned above and don't know whether to ignore it or not.
>
> Thanks for any help in advance,
> Dorthe
>