Preprocess error

[kokyriakidis]

Hello, I followed the R example but when I entered ProcessedData <- AMARETTO_Preprocess(DataSetDirectories) an error occurred:

Batch correction.
Error in TCGA_BatchCorrection_MolecularData(MA_TCGA, BatchData, MinPerBatch) : 
  argument "BatchData" is missing, with no default

any ideas?

[jayendrashinde91]

Hi!
Thanks for reaching out.
We have fixed the issue you mentioned and have pushed the latest update.
Running the following code should solve it for you now:
ProcessedData <- AMARETTO_Preprocess(DataSetDirectories,BatchData)
Best,
Jay

[kokyriakidis]

Hi, now it says:

Adjusting the Data
Loading MethylMix data.
	Getting MethylMix methylation states.
Error in eval(parse(text = paste("MET_TCGA=MethylStates$", CancerSite,  : 
  object 'MethylStates' not found

I specified as CancerSite LIHC

[jayendrashinde91]

Hi,

AMARETTO/AMARETTO_EXAMPLE/AMARETTO.R

Line 33 in ec2dddc

#load(inst/extdata//MethylStates.rda) #MethylMix preprocessed data for CancerSite

You need to load the MethylStates object to go ahead. We are constantly working on updating the package currently. And also a revised vignette will also be up for you to follow the package functions in a few days.
Thanks

[kokyriakidis]

The R example says:

#ProcessedData <- AMARETTO_Preprocess(DataSetDirectories,BatchData)

#load(inst/extdata//MethylStates.rda) #MethylMix preprocessed data for CancerSite
#ProcessedData[[3]] <- MethylStates[CancerSite] #MethylMix preprocessed data for CancerSite

#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
# Loading preprocessed TCGA-LAML example dataset:
#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
data("ProcessedDataLIHC")

#-----------------------------------------------------------------------------------------
# 4. Running AMARETTO
#-----------------------------------------------------------------------------------------
AMARETTOinit <- AMARETTO_Initialize(ProcessedDataLIHC,NrModules = 2, VarPercentage = 60)

1. So I load Methylstates first. Do I use this file for any kind of CancerSite?

2. Next, do I run ProcessedData <- AMARETTO_Preprocess(DataSetDirectories,BatchData) or something else from above?

3. What do I do next? ProcessedData[[3]] <- MethylStates[CancerSite] and then data("ProcessedDataLIHC")?

4. Then i run AMARETTOinit <- AMARETTO_Initialize(ProcessedDataLIHC,NrModules = 2, VarPercentage = 60) as it is? or I change ProcessedDataLIHC?