[BioC] Limma 1.6.1 : composite normalisation method not recommended
?? (+ function error)
Laetitia.Marisa at cgm.cnrs-gif.fr
Thu May 13 19:17:27 CEST 2004
I am trying to normalize my data from titration controls with the
First of all I would like to know why this method is not recommended
any more by the author (in a previous mail from Gordon Smyth).
Otherwise here is my problem if it is of any interest to go on with this
method : the function returns an error that has already been mentioned
in the mailing list but it seems to me that I don't have a problem with
my controlspots variable.
Here is the command line I am using :
nMA <- gif.normalizeWithinArrays(MA, layout=MA$printer,
where ctrlspots :
logi [1:864] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE
TRUE FALSE FALSE ...
and MA$M :
num [1:864, 1:6] -0.2679 -0.1382 1.3026 0.0359 -0.9560 ...
The error returned is :
Number of Observations: 192
Equivalent Number of Parameters: 4.95
Residual Scale Estimate: 0.12
Error in predLoess(object$y, object$x, newx, object$s, object$weights, :
NA/NaN/Inf in foreign function call (arg 3)
This error comes from the predict function : predict(fit, newdata=x)
There are infinite values in x in my data and in the function there no
Thanks a lot,
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