virtualArrayLoadRaw: Load user provided raw data files in the virtualArray...
In virtualArray: Build virtual array from different microarray platforms

Description Usage Arguments Details Value Author(s) See Also Examples

This function loads all raw data files provided by the user in the virtualArray directory structure, that was created by virtualArrayDirs in the first place.

1	virtualArrayLoadRaw(root_dir = getwd(), affy_sum = "rma")

`root_dir`	The top level directory holding the rawdata and the "sample_info.txt" file.
`affy_sum`	Select the summerization method to use for Affymetrix chips; defaults to "RMA".

The function first reads in the virtualArray directory including raw data files. Based on this a "sample_info" data.frame is created holding information about chip type and the corresponding file name. Then "sample_info" is checked for the presence of certain microarray platforms. If present, the function loads raw data of all platforms. The "sample_info" data.frame is exported to "sample_info.txt". It is up to the user to change the values of the "Covariate 1" column to something meaningful, thus providing the additional information for the batch effect removal in the final step of the process.

This function does not return a value, but creates objects in the current environment holding raw data of every provided chip type. The objects are named "rawdata_*". Where "*" is the chip type.

Andreas heider (2011)

virtualArray-package, virtualArray.ExpressionSet, virtualArrayCompile