Thanks Martin, It is very helpful, Wayne -- Martin Morgan wrote: > Hi Wayne -- > > Wayne Xu <wxu at="" msi.umn.edu=""> writes: > > >> Hello, >> >> I created a filter function to filter the microarray data set by row >> variance, but got follow error: >> >> > dim(data1) >> [1] 7129 38 >> > data1[1,2:4] >> data[, 4] data[, 6] data[, 8] >> 1 -139 -76 -135 >> >> >> > myfilter<-function(j){ >> + function(x){ >> + rowVars(x)<j>> + } >> + } >> > >> > ff<-filterfun(myfilter(20)) >> > filt<-genefilter(data1,ff) >> Error in rowSums(!is.na(x)) : >> 'x' must be an array of at least two dimensions >> > > genefilter feeds the filter function each row as a simple vector, so > try > > myfilter = function(j) function(x) var(x) < j > > Here's what I did... > > >> m = matrix(1:20, 5) >> myfilter = function(j) function(x) rowVars(x) < j >> options(error=recover) >> genefilter(m, filterfun(myfilter(2))) >> > genefilter(m, filterfun(myfilter(2))) > Error in rowSums(!is.na(x)) : > 'x' must be an array of at least two dimensions > > Enter a frame number, or 0 to exit > > 1: genefilter(m, filterfun(myfilter(2))) > 2: apply(expr, 1, flist) > 3: FUN(newX[, i], ...) > 4: fun(x) > 5: rowVars(x) > 6: rowSums(!is.na(x)) > > Selection: 4 > Called from: eval(expr, envir, enclos) > Browse[1]> x > [1] 1 6 11 16 # Aha, a vector not a matrix with 1 row! > Browse[1]> Q > >> options(error=NULL) >> > > Hope that helps, > > Martin > > >> I know the error occurred in: >> > rowSums >> function (x, na.rm = FALSE, dims = 1) >> { >> if (is.data.frame(x)) >> x <- as.matrix(x) >> if (!is.array(x) || length(dn <- dim(x)) < 2) >> stop("'x' must be an array of at least two dimensions") >> if (dims < 1 || dims > length(dn) - 1) >> stop("invalid 'dims'") >> p <- prod(dn[-(1:dims)]) >> dn <- dn[1:dims] >> z <- if (is.complex(x)) >> .Internal(rowSums(Re(x), prod(dn), p, na.rm)) + (0+1i) * >> .Internal(rowSums(Im(x), prod(dn), p, na.rm)) >> else .Internal(rowSums(x, prod(dn), p, na.rm)) >> if (length(dn) > 1) { >> dim(z) <- dn >> dimnames(z) <- dimnames(x)[1:dims] >> } >> else names(z) <- dimnames(x)[[1]] >> z >> } >> <environment: namespace:base=""> >> >> I wrote other filters and they work fine, but the rowVars or rowSums >> function does not work for me. >> >> Can someone help? Thanks in advance ! >> >> Wayne >> > >