The
Affymetrix CN CHP Input Engine
imports multiple CNCHP and/or LOHCHP files into a single SAS data set with rows representing
probeset
identifiers and columns containing various copy number and/or
loss of heterozygosity
measurements for each of the samples.
|
•
|
The folder containing the
.cnchp
files obtained by processing SNP
.cel
files using the Affymetrix Genotyping Console. These
.cnchp
files, each corresponding to an individual
microarray
, contain summarized copy number information and specific information about the format of the chip.
|
|
•
|
The
Experimental Design File (EDF)
for the experiment. The EDF lists specific information about the design of the experiment. The EDF is typically a text file or Excel spread sheet and must be created before the data can be imported. The edf_cn5_2obs.sas7bdat EDF used in the following example, was generated using the
Create a Design Data Set from an Existing Data Set
process. This EDF was placed in a new
Copy Number
folder that was created in the
Sample Data
folder that comes with JMP Genomics.
|
The following example uses CNCHP files created from
.cel
files in Affymetrix Genotyping Console, from an X titration data set available for download from
Affymetrix
. Two compressed files,
NA01416_5X.rep1.CN5.cnchp
and
NA01416_5X.rep2.CN5.cnchp
, containing LOH and CN data, were downloaded from the
Affymetrix website
, unzipped, and saved to a folder named
Copy Number
, located in the
Sample Data
folder that comes with JMP Genomics.
For detailed information about the files and data sets used or created by JMP Life Sciences software, see
Files and Data Sets
.
The output data sets generated by this process are listed in a
Results
window. Refer to the
Affymetrix Copy Number CHP Input Engine
output documentation for detailed descriptions.