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 |
Log2 ratio (signal / median of Reference signal). |
|
WeightedLog2Ratio |
Float |
Running median of log2 ratios for n markers (default: n = 5). |
|
SmoothSignal |
Float |
Each value is the result of a kernel smooth over a window of genomically contiguous log2 ratios. By default, this is converted to a copy number value using a log-linear model that fits each CN state to its expected log2 ratio. This is useful for seeing mosaics. |
For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.
To Specify a Copy Number Data Set:
| 8 | Type the name of the data set into the text field. |
| 8 | If you change your mind and would like to reset the field, click . |