[BioC] [combat] Re: Error in FUN(newX[, i], ...) : missing observations in cov/c

[Marc-Danie Jessica Nazaire]

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
>
>  
>  -- 
>
>  
>