If you bring in Affymetrix data which has been normalized by some other software, this tool converts the data to Chipster format (by adding the text "chip." in front of the expression value columns, adds annotation information (if the chiptype is specified) and generates the phenodata file.
The normalized data file needs to be imported to Chipster using the Import tool. Every column containing normalized expression values need to be specified as Sample in the Import tool and the Affymetrix probe ID as Identifier. It is possible to use other types of identifier as well, like gene symbol Entrez ID or similar, but no additional annotation information will be added in this step.
If you want to be able to use analysis tools requiring annotation information, you need to specify the chiptype using the chip's annotation package name (they are listed in brackets after the chip name here)
Parameters keep.annotation and keep.flags control whether or not annotation and/or flag columns are kept or discarded after preprocessing. If these options are used, each file should have a column called flag/Flag and containing flag-information and/or a column called annotation/Annotation and containing the annotation-information. Please note that gene symbol information associated with the given chiptype will be replaced by data-specific annotations (give in the annotation/Annotation column), if both the keep.annotations and the chiptype have been set up.
A new normalized dataset and a phenodata file.