Import expression data from the Affymetrix CHP format to SelTag data file.

Data specification

The input for CHPImport is the set of expression data in Affymetrix CHP data format, corresponding CDF file and file with list of CHP files to be processed and their short description (this file is provided by user). The CHP data already processed by statistical algorithm. The output is SelTag data file with gene expression data.

The program can read a set of CHP data files for the same chip. The output file is in Seltag format and reports the #HEADER section: Experiment filename; Algorithm name, DataHeader as reported in the CEL file, DataScalingFactor (sf value), DataNormalizationFactor (nf value), DataSignalTrimmedMean.

Example of experiment list file

GSM42890	DEHP_48hr_Veh1	DEHP 48hr Veh1
GSM42891	DEHP_48hr_Veh2	DEHP 48hr Veh2
GSM42892	DEHP_48hr_Veh3	DEHP 48hr Veh3
GSM42893	DEHP_48hr_Veh4	DEHP 48hr Veh4
GSM42894	DEHP_48hr_Veh5	DEHP 48hr Veh5

This file contains three columns separated by symbol. First column is the experiment data name (the corresponding CEL file should start from this name and have extension *.chp, for example GSM42890.chp). Second column is the name of the variable in the output SelTag file, corresponding to this experiment (see below example of SelTag output file). This column should not contain spaces. Third column is the extended description of the experiment that will appear at the SelTag file header section.

Example of output data

#HEADER
Import expression data from the set of CHP files.
  1 ExperimentDataFilename=GSM42883.cel
  1 DataHeader=Clof_168hr_t	Clof 168hr treated POOLED
  1 Algorithm name:ExpressionStat
  1 Algorithm parameters:BF= Alpha1=0.04 Alpha2=0.06 Tau=0.015 Gamma1H=0.0025 Gamma1L=0.0025 Gamma2H=0.003 Gamma2L=0.003 Perturbation=1.1 TGT=1500 NF=1.000000 SF=29.560343 SFGene=All 
  1 Algorithm summary:Background=Avg:29.82,Stdev:1.12,Max:32.6,Min:27.2 Noise=Avg:1.02,Stdev:0.05,Max:1.2,Min:0.9 RawQ=0.98 
  1 Algorithm ver:5.0
  1 Program:GeneChipAnalysis.GEBaseCall.1
  1 Probe array type:RG_U34A 
#ENDHEADER
ProbesetName	STRING
Clof_168hr_t_Signal	FVALUE
Clof_168hr_t_Detection	WORD
Clof_168hr_t_Detection_p	FVALUE
END
DATA
AFFX-MurIL2_at	37.5396	A	0.78955	
AFFX-MurIL10_at	51.8929	A	0.60308	
AFFX-MurIL4_at	5.7568	A	0.97607	
AFFX-MurFAS_at	32.2922	A	0.60308	
AFFX-BioB-5_at	714.0201	A	0.08359
AFFX-BioB-M_at	1563.2017	P	0.00125
AFFX-BioB-3_at	800.5414	P	0.00359
AFFX-BioC-5_at	3686.6155	P	0.00017
AFFX-BioC-3_at	1989.3492	P	0.00006
AFFX-BioDn-5_at	2807.6296	P	0.00066
AFFX-BioDn-3_at	16410.8984	P	0.00020
AFFX-CreX-5_at	32975.3750	P	0.00004