I used the
prcomp() function to perform a PCA analysis in R. However, there's a bug in that function such that the
na.action parameter does not work. I asked for help on stackoverflow; two users there offered two different ways of dealing with
NA values. However, the problem with both solutions is that when there is an
NA value, that row is dropped and not considered in the PCA analysis. My real data set is a matrix of 100 x 100 and I do not want to lose a whole row just because it contains a single
The following example shows that the
prcomp() function does not return any principal components for row 5 as it contains a
d <- data.frame(V1 = sample(1:100, 10), V2 = sample(1:100, 10), V3 = sample(1:100, 10)) result <- prcomp(d, center = TRUE, scale = TRUE, na.action = na.omit) result$x # $ d$V1 <- NA # $ result <- prcomp(~V1+V2, data=d, center = TRUE, scale = TRUE, na.action = na.omit) result$x
I was wondering if I can set the
NA values to a specific numerical value when
scale are set to
TRUE so that the
prcomp() function works and does not remove rows containing
NA's, but also does not influence the outcome of the PCA analysis.
I thought about replacing
NA values with the median value across a single column, or with a value very close to 0. However, I am not sure how that influences the PCA analysis.
Can anybody think of a good way of solving that problem?