Error using impute.knn function
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@peter-davidsen-4584
Last seen 6.0 years ago
Dear List, After quantile normalizing some Agilent microarray data I end up with a data matrix containing missing values (as I choose to log2 transform my matrix just before the normalization step). Thus, I want to use the impute.knn() function in the impute package... however, I keep getting an error that I haven't been able to solve. > data.qnorm <- normalize.quantiles(log2(raw.filt)) Warning message: In normalize.quantiles(log2(raw.filt)) : NaNs produced > ok <- complete.cases(data.qnorm) > sum(!ok) [1] 1897 > NA.probes <- apply(data.qnorm, 1, function(x)length(which(is.finite(x) == FALSE))) > table(NA.probes) NA.probes 0 1 2 3 4 59123 2379 145 9 1 > > qnorm.impute <- impute.knn(data.qnorm) Error in twomeans.miss(x) : NA/NaN/Inf in foreign function call (arg 1) Calls: impute.knn ... knnimp -> knnimp.split -> twomeans.miss -> .Fortran > traceback() 5: .Fortran("twomis", x, as.integer(p), as.integer(n), imiss, double(2 * n), integer(2 * n), as.integer(maxit), as.double(eps), as.integer(starters), cluster = integer(2 * p), nsize = integer(2), double(2 * p), ratio = double(1), iter = integer(1), integer(p), integer(n), PACKAGE = "impute") 4: twomeans.miss(x) 3: knnimp.split(x, k, imiss, irmiss, p, n, maxp = maxp) 2: knnimp(x, k, maxmiss = rowmax, maxp = maxp) 1: impute.knn(data.qnorm) Any inputs are appreciated. Regards, Peter > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] impute_1.30.0 preprocessCore_1.18.0 marray_1.34.0 limma_3.12.1 [5] BiocInstaller_1.4.7 loaded via a namespace (and not attached): [1] tools_2.15.1
Microarray Normalization impute Microarray Normalization impute • 1.6k views
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Entering edit mode
@peter-davidsen-4584
Last seen 6.0 years ago
Dear List, After quantile normalizing some Agilent microarray data I end up with a data matrix containing missing values (as I choose to log2 transform my matrix just before the normalization step). Thus, I want to use the impute.knn() function in the impute package... however, I keep getting an error that I haven't been able to solve. > data.qnorm <- normalize.quantiles(log2(raw.filt)) Warning message: In normalize.quantiles(log2(raw.filt)) : NaNs produced > ok <- complete.cases(data.qnorm) > sum(!ok) [1] 1897 > NA.probes <- apply(data.qnorm, 1, function(x)length(which(is.finite(x) == FALSE))) > table(NA.probes) NA.probes 0 1 2 3 4 59123 2379 145 9 1 > > qnorm.impute <- impute.knn(data.qnorm) Error in twomeans.miss(x) : NA/NaN/Inf in foreign function call (arg 1) Calls: impute.knn ... knnimp -> knnimp.split -> twomeans.miss -> .Fortran > traceback() 5: .Fortran("twomis", x, as.integer(p), as.integer(n), imiss, double(2 * n), integer(2 * n), as.integer(maxit), as.double(eps), as.integer(starters), cluster = integer(2 * p), nsize = integer(2), double(2 * p), ratio = double(1), iter = integer(1), integer(p), integer(n), PACKAGE = "impute") 4: twomeans.miss(x) 3: knnimp.split(x, k, imiss, irmiss, p, n, maxp = maxp) 2: knnimp(x, k, maxmiss = rowmax, maxp = maxp) 1: impute.knn(data.qnorm) Any inputs are appreciated. Regards, Peter > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] impute_1.30.0 preprocessCore_1.18.0 marray_1.34.0 limma_3.12.1 [5] BiocInstaller_1.4.7 loaded via a namespace (and not attached): [1] tools_2.15.1
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