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I am trying to do PCA on data frame with 5000 columns and 30 rows Sample <- read.table(file.choose(), header=F,sep="\t") Sample.scaled <- data.frame(apply(Sample,2,scale)) pca.Sample <- prcomp(Sample.scaled,retx=TRUE)` Got the error Error in svd(x, nu = 0) : infinite or missing values in 'x' sum(is.na(Sample)) [1] 0 sum(is.na(Sample.scaled)) [1] 90 Tried to ignore all na values by using the following pca.Sample <- prcomp(na.omit(Sample.scaled),retx=TRUE) Which gives the following error Error in svd(x, nu = 0) : 0 extent dimensions There were reports that na.action requires formula to be given and hence tried the below pca.Sample <- prcomp(~.,center=TRUE,scale=TRUE,Sample, na.action=na.omit) Now getting the following error Error in prcomp.default(x, ...) : cannot rescale a constant/zero column to unit variance Think that the problem might be because "One of my data columns is constant. The variance of a constant is 0, and scaling would then divide by 0, which is impossible." But not sure on how to tackle this. Any help much appreciated ....

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