genefilter problem
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@wxumsiumnedu-1819
Last seen 9.6 years ago
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 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 --
Microarray Microarray • 1.6k views
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@martin-morgan-1513
Last seen 6 weeks ago
United States
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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793
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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 >> > >
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