edammer / tampor Goto Github PK

Hi Eric,

I tried running my data through TAMPOR. The normalization finishes, but no result is returned due to the error:

...Reached convergence criterion (Frobenius Norm Difference)<1e-8!
Error in `[.data.frame`(ratioCleanDatUnnorm, , match(rownames(traits),  : 
undefined columns selected

My call to TAMPOR looks like:

TAMPOR_results <- TAMPOR(
   dat = cleanDat,
   traits = traits,
   noGIS = FALSE, 
   useAllNonGIS = FALSE, 
   batchPrefixInSampleNames = TRUE, 
   GISchannels = controls$channel,  
   iterations = 250,
   samplesToIgnore = "NONE", 
   meanOrMedian = "median", 
   removeGISafter = FALSE, 
   minimumBatchSize = 5, 
   parallelThreads=2, 
   outputSuffix = "TAMPOR", 
   path=getwd()
   )

I'll send you an email with cleanDat.Rds and traits.Rds so you can try to reproduce the error.

This error appears when a large input data set (dat data frame or matrix input) includes many zeros or negative values on one row. The code should convert them to NA after displaying the first 10 bad rows. The error is being thrown by code trying to display these rows of dat as comma separated strings.

For now, one can avert the error by pre-cleaning dat input as follows:

dat[dat<=0] <- NA