Copy Number Data Set

Name the SAS data set created from input files.

When this field is left empty , the specified name of the Output Experimental Design Data Set concatenated with " _data " is applied.

Caution : Names longer than 32 characters are truncated.

The Copy Number Data Set includes the following columns:

Column Name	Column Type	Description
ProbeSetName	ASCII	The name of the probeset .
Chromosome	UByte	The chromosome display values (1-22, X, Y, and MT) are stored in the data set header. The values in this column are defined as: 1 - 22 , 24 (for X), 25 (for Y), 26 (for MT) and 255 (for no value).
Position	UInt	Genomic position in the chromosome.
Log2Ratio	Float	Log 2 ratio (signal / median of Reference signal).
WeightedLog2Ratio	Float	Running median of log 2 ratios for n markers (default: n = 5).
SmoothSignal	Float	Each value is the result of a kernel smooth over a window of genomically contiguous log 2 ratios. By default, this is converted to a copy number value using a log-linear model that fits each CN state to its expected log 2 ratio. This is useful for seeing mosaics.

For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets .

To Specify a Copy Number Data Set:

Type the name of the data set into the text field.

If you change your mind and would like to reset the field, click Clear .