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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