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Sage-Bionetworks / CMSclassifier

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naImpute fails: "names do not match previous names" #5

Open ptsant opened 6 years ago

ptsant commented 6 years ago

Hello,

I noticed that naImpute() fails (R 3.3.2, x86_64-apple-darwin13.4.0 (64-bit)) at rbind():

debugging in: naImpute(expmat.prip.ez, listModelGenes("RF")) debug: { m <- rowMeans(Exp, na.rm = T) mm <- mean(m, na.rm = T) m[which(is.na(m))] <- mm mna <- rowMeans(Exp) w <- which(is.na(mna)) for (i in w) { try(Exp[i, which(is.na(Exp[i, ]))] <- m[i]) } G <- setdiff(G, rownames(Exp)) if (!is.null(G)) { tmp <- as.data.frame(array(mm, dim = c(length(G), ncol(Exp)))) rownames(tmp) <- G names(tmp) <- names(Exp) Exp <- rbind(Exp, tmp) } Exp } Browse[2]> q() Warning message: In q() : cannot quit from browser Browse[2]> Q naImpute(expmat.prip.ez, listModelGenes("RF")) debugging in: naImpute(expmat.prip.ez, listModelGenes("RF")) debug: { m <- rowMeans(Exp, na.rm = T) mm <- mean(m, na.rm = T) m[which(is.na(m))] <- mm mna <- rowMeans(Exp) w <- which(is.na(mna)) for (i in w) { try(Exp[i, which(is.na(Exp[i, ]))] <- m[i]) } G <- setdiff(G, rownames(Exp)) if (!is.null(G)) { tmp <- as.data.frame(array(mm, dim = c(length(G), ncol(Exp)))) rownames(tmp) <- G names(tmp) <- names(Exp) Exp <- rbind(Exp, tmp) } Exp } Browse[2]> n debug: m <- rowMeans(Exp, na.rm = T) Browse[2]> n debug: mm <- mean(m, na.rm = T) Browse[2]> n debug: m[which(is.na(m))] <- mm Browse[2]> n debug: mna <- rowMeans(Exp) Browse[2]> n debug: w <- which(is.na(mna)) Browse[2]> n debug: for (i in w) { try(Exp[i, which(is.na(Exp[i, ]))] <- m[i]) } Browse[2]> n debug: G <- setdiff(G, rownames(Exp)) Browse[2]> n debug: if (!is.null(G)) { tmp <- as.data.frame(array(mm, dim = c(length(G), ncol(Exp)))) rownames(tmp) <- G names(tmp) <- names(Exp) Exp <- rbind(Exp, tmp) } Browse[2]> n debug: tmp <- as.data.frame(array(mm, dim = c(length(G), ncol(Exp)))) Browse[2]> n debug: rownames(tmp) <- G Browse[2]> n debug: names(tmp) <- names(Exp) Browse[2]> n debug: Exp <- rbind(Exp, tmp) Browse[2]> n Error in match.names(clabs, names(xi)) : names do not match previous names`

This can be rectified by replacing names(tmp) <- names(Exp) with colnames(tmp) <- colnames(Exp).

vllorens commented 4 years ago

Thanks for posting this, saved me quite some time from debugging myself