[BioC] limma and composite normalization method

Diego Díez Ruiz ddiez at iib.uam.es
Tue Jul 13 11:37:22 CEST 2004

Hello all,

I'm trying to use the composite method on limma_1.7.2 but I get an error 
when I normalizeWithinArrays:

Error in predLoess(object$y, object$x, newx, object$s, object$weights,  :
         NA/NaN/Inf in foreign function call (arg 3)

I have NA values in my data. The "loess" function can handle NA's as it 
is done in normalizeWithinArrays:

fit <- loess(y ~ x, weights = w, span = span, subset = controlspots,
                 na.action = na.exclude, degree = 0, surface = "direct",
                 family = "symmetric", trace.hat = "approximate",
                 iterations = iterations)

but I can't see the same to the "predict" function. I overrided that 
modifing normalizeWithinArrays as:

global <- predict(fit, newdata = x)
global <- predict(fit, newdata = x[!is.na(x)])

¿Is this a correct way to do that or did I miss something?

Thanks in advance,


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