Hi,

I'm using the ComBat package within the MSPrep R package to normalize some metabolomic data. I receive the following error when trying to run MSPrep:

Error in while (change > conv) { : missing value where TRUE/FALSE needed

I traced this error to the ComBat function and within it, the it.sol function, the code for which I obtained from the ComBat website (http://www.bu.edu/jlab/wp-assets/ComBat/Download.html) and have pasted below.

it.sol  <- function(sdat,g.hat,d.hat,g.bar,t2,a,b,conv=.0001){
        n <- apply(!is.na(sdat),1,sum)
        g.old <- g.hat
        d.old <- d.hat
        change <- 1
        count <- 0
        while(change>conv){
               g.new <- postmean(g.hat,g.bar,n,d.old,t2)
               sum2 <- apply((sdat-g.new%*%t(rep(1,ncol(sdat))))^2, 1, sum,na.rm=T)
               d.new <- postvar(sum2,n,a,b)
               change <- max(abs(g.new-g.old)/g.old,abs(d.new-d.old)/d.old)
               g.old <- g.new
               d.old <- d.new
               count <- count+1
               }
        #cat("This batch took", count, "iterations until convergence\n")
        adjust <- rbind(g.new, d.new)
        rownames(adjust) <- c("g.star","d.star")
        adjust
        }

The MSPrep package passes the following arguments through the function:

for (i in 1:n.batch) {
    temp <- it.sol(s.data[, batches[[i]]], gamma.hat[i, ], delta.hat[i,
        ], gamma.bar[i], t2[i], a.prior[i], b.prior[i])
    gamma.star <- rbind(gamma.star, temp[1, ])
    delta.star <- rbind(delta.star, temp[2, ])
}

Where n.batch=50, the dimensions of s.data are (392, 300), the dimensions of gamma.hat (g.hat) are (50, 392), the dimensions of delta.hat (d.hat) are (50, 392), gamma.bar (g.bar) is NULL, a.prior (a) is NULL, and b.prior (b) is null).

I believe the problem is coming from the fact that gamma.bar is null, which results because gamma.hat has NaN values.

Could you please advise?

Thank you,

Anna

Anna Reisetter, MS
Statistical Analyst/Programmer
Department of Preventive Medicine
Northwestern University Medical School
680 N. Lake Shore Drive Suite 1400
Chicago, IL 60611
312 503 7039
anna.reisetter@northwestern.edu<mailto:anna.reisetter@northwestern.edu>


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