Can you email me a 'toy' example with your data of the failure?


On May 10, 2013, at 2:01 PM, Marc-Danie Jessica Nazaire wrote:

No, I am not.

Marc-Danie

On Friday, May 10, 2013 1:57:50 PM UTC-4, Evan Johnson wrote:
Are you using the 'sva' package version or the R script?


On May 10, 2013, at 1:51 PM, Marc-Danie Jessica Nazaire wrote:

Hi Igor,

We are getting this error when running ComBat with no covariates specified (runs successfully with covariates) but there are no non-numeric or missing values in our dataset.

I did some debugging and tracked down the error to this piece of code:
if (!NAs){gamma.hat <- solve(t(batch.design)%*%batch.design)%*%t(batch.design)%*%t(as.matrix(s.data))}else{gamma.hat=apply(s.data,1,Beta.NA,batch.design)}

NOTE: s.data and batch.design have no NAs

The gamma.hat matrix has NAs after this calculation and fails later during the call:
gamma.bar <- apply(gamma.hat, 1, mean)


Do you have any more ideas or insights on what could be causing this error?

Thanks,
Marc-Danie

On Tuesday, June 9, 2009 2:57:40 PM UTC-4, Evan wrote:
If you see the "Error in FUN(newX[, i], ...) : missing observations in
cov/cor" error message while running ComBat, search for non-numeric
or
missing values in your data file. It will work fine when you fixed
them.

Igor

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