{{FAQ
entrydate=January 18, 2011 |
topic=caArray Usage |
Qtext= |
- Chip Lot #, Hybridization Date, Chip Status (Good, Dim, Scratch, Background, Bad-Other) - For all types of arrays
- cQC, QC call rate, - For SNP 6.0 arrays
- AUC - For Gene 1.0 ST/Exon 1.0 ST arrays
- Noise, Scale Factor, %P - For 3'IVT arrays
- % Probe set present - For miRNA arraysshrivass
Original post on the ForumAtext=
The QC data as mentioned in the question can be added as Comment[] columns in your MAGE-TAB SDRF.
Ideally, they would be Characteristics associated with the Hybridization Name or Scan Name column. Unfortunately, the MAGE-TAB specification does not allow Characteristic) columns for Hybridization Name or Scan Name. We recommend that you include these QC annotations as Comment( columns following either the Hybridization Name or Scan Name column.
One thing to keep in mind is that caArray does not currently parse the contents of Comment[] columns and store the values in the database. But these annotations would be captured in the SDRF file itself, which is stored as is by caArray.
}}