Hi, This has been asked a few times but I'm unable to find an answer. When you run >esetgcrma2 <- gcrma(data, fast=FALSE) #OR esetgcrma2 <- justGCRMA(fast=FALSE) #You get this error Adjusting for optical effect......Done. Adjusting for non-specific binding.Error in bg.adjust.fullmodel(pms[, i], mms[, i], pm.affinities, mm.affinities, : couldn't find function "gcrma.bg.transformation" I did some investigating and it seems that gcrma.bg.transformation called in the last lines of bg.adjust.fullmodel is not a defined function, whilst gcrma.bg.transformation.fast is. Is there a reason for this? This also happens in 1.9 and my previous 2.0 devel, but I've been waiting for the new release of BioC in case it had been fixed (I'm running 2.0, 1.5, win2k). Anyone provide a quick fix? Cheers, Matt > bg.adjust.fullmodel function (pms, mms, pm.affinities, mm.affinities, index.affinities, k = 6 * fast + 0.25 * (1 - fast), Q = 0.25, Qmm = 0.5, rho = 0.7, fast = TRUE) { parameters <- bg.parameters.ns(pms[index.affinities], pm.affinities, mm.affinities) mu.pm <- vector("numeric", length(pms)) sigma <- vector("numeric", length(pms)) mu.pm[index.affinities] <- parameters$bg.mu sigma[index.affinities] <- parameters$bg.sigma parameters <- bg.parameters.ns(mms[index.affinities], mm.affinities, mm.affinities) mu.mm <- vector("numeric", length(pms)) mu.mm[index.affinities] <- parameters$bg.mu if (length(index.affinities) < length(pms)) { mu.pm[-index.affinities] <- medianmu.pm[index.affinities]) mu.mm[-index.affinities] <- medianmu.mm[index.affinities]) sigma[-index.affinities] <- median(sigma[index.affinities]) } if (fast) { bhat <- expmu.pm + rho * (log(mms) - mu.mm) + 1/2 * (1 - rho^2) * sigma^2) var.y = exp(2 * mu.pm + sigma^2) * (exp(sigma^2) - exp(sigma^2 * rho^2)) return(gcrma.bg.transformation.fast(pms, bhat, var.y, k = k)) } else return(gcrma.bg.transformation(pms, mu.pm + rho * (log(mms) - mu.mm), sqrt(1 - rho^2) * sigma, k = k)) } > gcrma.bg.transformation.fast function (x, bhat, var.y, k) { x <- x - bhat Index <- x > 0 x[!Index] <- 0 alpha <- rep(0, length(x)) xplusk <- x[Index] + k logxplusk <- log(xplusk) alpha[Index] <- (logxplusk - log(k)) * (logxplusk - log(k) + k/xplusk)/((logxplusk - log(k) + k/xplusk)^2 + var.y[Index]/xplusk^2) y <- exp(alpha * log(x + k) + (1 - alpha) * log(k)) } > gcrma.bg.transformation Error: Object "gcrma.bg.transformation" not found

sorry about that. I've attached the missing file here and will try to added to the devel package On Tue, 2 Nov 2004, Matthew Hannah wrote: > Hi, > > This has been asked a few times but I'm unable to find an answer. When > you run > >esetgcrma2 <- gcrma(data, fast=FALSE) > #OR > esetgcrma2 <- justGCRMA(fast=FALSE) > #You get this error > Adjusting for optical effect......Done. > Adjusting for non-specific binding.Error in bg.adjust.fullmodel(pms[, > i], mms[, i], pm.affinities, mm.affinities, : > couldn't find function "gcrma.bg.transformation" > > I did some investigating and it seems that gcrma.bg.transformation > called in the last lines of bg.adjust.fullmodel is not a defined > function, whilst gcrma.bg.transformation.fast is. Is there a reason for > this? > > This also happens in 1.9 and my previous 2.0 devel, but I've been > waiting for the new release of BioC in case it had been fixed (I'm > running 2.0, 1.5, win2k). > > Anyone provide a quick fix? > > Cheers, > Matt > > > > > bg.adjust.fullmodel > function (pms, mms, pm.affinities, mm.affinities, index.affinities, > k = 6 * fast + 0.25 * (1 - fast), Q = 0.25, Qmm = 0.5, rho = 0.7, > fast = TRUE) > { > parameters <- bg.parameters.ns(pms[index.affinities], pm.affinities, > > mm.affinities) > mu.pm <- vector("numeric", length(pms)) > sigma <- vector("numeric", length(pms)) > mu.pm[index.affinities] <- parameters$bg.mu > sigma[index.affinities] <- parameters$bg.sigma > parameters <- bg.parameters.ns(mms[index.affinities], mm.affinities, > > mm.affinities) > mu.mm <- vector("numeric", length(pms)) > mu.mm[index.affinities] <- parameters$bg.mu > if (length(index.affinities) < length(pms)) { > mu.pm[-index.affinities] <- medianmu.pm[index.affinities]) > mu.mm[-index.affinities] <- medianmu.mm[index.affinities]) > sigma[-index.affinities] <- median(sigma[index.affinities]) > } > if (fast) { > bhat <- expmu.pm + rho * (log(mms) - mu.mm) + 1/2 * > (1 - rho^2) * sigma^2) > var.y = exp(2 * mu.pm + sigma^2) * (exp(sigma^2) - exp(sigma^2 * > > rho^2)) > return(gcrma.bg.transformation.fast(pms, bhat, var.y, > k = k)) > } > else return(gcrma.bg.transformation(pms, mu.pm + rho * (log(mms) - > mu.mm), sqrt(1 - rho^2) * sigma, k = k)) > } > > > > gcrma.bg.transformation.fast > function (x, bhat, var.y, k) > { > x <- x - bhat > Index <- x > 0 > x[!Index] <- 0 > alpha <- rep(0, length(x)) > xplusk <- x[Index] + k > logxplusk <- log(xplusk) > alpha[Index] <- (logxplusk - log(k)) * (logxplusk - log(k) + > k/xplusk)/((logxplusk - log(k) + k/xplusk)^2 + > var.y[Index]/xplusk^2) > y <- exp(alpha * log(x + k) + (1 - alpha) * log(k)) > } > > > > gcrma.bg.transformation > Error: Object "gcrma.bg.transformation" not found > -------------- next part -------------- gcrma.bg.transformation <- function(pms,mu,tau,k,lower.bound=.5,a=1,...){ step=60 base=exp(log(2^16)/step)#defult~=1.2 mylog=function(x) log(x,base) K0=max(0,round(mylog(lower.bound))+1) Ks=floor(mylog(pms)) posty <- function(xxx){ p=xxx[1];mu=xxx[2];tau=xxx[3];K=xxx[4] pnorms=pnorm(log(p-base^(K0:K)),mu,tau) diff.pnorms=pnorms[-length(pnorms)]-pnorms[-1] g=(base^a+1)/base^(a*(K0:(K-1)+1))/2*diff.pnorms g0=(1/lower.bound^a+1/base^(a*K0))/2*(pnorm(log(p-lower.bound),mu, tau)-pnorm(log(p-base^K0),mu,tau)) gn=(base^a+1)/base^(a*(K+1))*pnorm(log(p-base^K),mu,tau) f=g*log(base^(K0:(K-1))*(base+1)/2);f2=g*log(base^(K0:(K-1))*(base +1)/2)^2 f0=g0*log(lower.bound/2+base^K0/2);f02=g0*log(lower.bound/2+base^K 0/2)^2 fn=gn*log(base^K/2+p/2);fn2=gn*log(base^K/2+p/2)^2 (sum(f)+f0+fn)/(sum(g)+g0+gn) } pm=apply(cbind(pms,mu,tau,Ks),1,posty) pm=exp(pm) pm[is.na(pm)]=lower.bound #with extreme mm>>>pm it's possible to get NaN pm }