Troubleshooting: Setup of directory structures

Author: Henrik Bengtsson
Created on: 2010-08-05

Last updated on: 2011-02-04

annotationData/

To assert that you have the correct directory structure for your annotation data, run the below script. If there is an error in your structure, then the error message will tell you so and where it is incorrect.

library("R.utils")

# For all aroma setups
pathAC <- Arguments$getReadablePath("annotationData/chipTypes/", mustExist=TRUE)

# Specific to your chip type
chipType <- "HuEx-1_0-st-v2,Ensembl,exon"
chipTypeS <- gsub(",.*", "", chipType)
path <- Arguments$getReadablePath(chipTypeS, path=pathAC, mustExist=TRUE)

# Check that the annotation files are there
print(list.files(path=path));

rawData/

To assert that you have the correct directory structure for your raw data, run the below script. If there is an error in your structure, then the error message will tell you so and where it is incorrect.

library("R.utils")

```r
# For all aroma setups
pathR <- Arguments$getReadablePath("rawData/", mustExist=TRUE)

# Specific to your data set and chip type
dataSet <- "Affymetrix-HeartBrain"
pathD <- Arguments$getReadablePath(dataSet, path=pathR, mustExist=TRUE)

chipType <- "HuEx-1_0-st-v2,Ensembl,exon"
chipTypeS <- gsub(",.*", "", chipType)
pathDC <- Arguments$getReadablePath(chipTypeS, path=pathD, mustExist=TRUE)

Check that the data files are there

print(list.files(path=pathDC))