User guide

ManualsBrandsSimplay Labs ManualsComputer equipmentiScan Duo

iScan System User Guide 57

Generated Files

Afterimagesarescanned,theyareregistered andintensitiesareextractedforeverybead

type.IftheAutoConvertfeaturewasenabled,ICSnormalizestheintensitydataand

generatesgenotypecalls.

` Registration—Registrationidentifiesbeadsbycorrelatingtheirlocationsonthe

scannedimagewithinformationinthebeadmap(*.dmap)file.

` IntensityData—Intensityextractionistheprocessby whichintensityvaluesare

determinedforeverybeadontheimage.Statisticsaregeneratedforeverybeadtype

basedontheintensitiesofthereplicatebeadsforthattype.Extractedinformationis

savedinintensitydata(*.idat)files.

` NormalizedData—IftheAutoConvertfeaturewasenabledforthescan,ICS

normalizesthedatainyour*.idatfilesandgeneratesgenotypecallsfromthe

normalizeddata.Thenormalizeddataandgenotypeca llsaresavedingenotypecall

(*.gtc)files.(See

GeneratingNormalizedDataandGenotypeCallsonpage37.)

The*.idatand(ifapplicable)*.gtcfilesaresavedontheiScanSystemcomputeror

networkundertheArrayID(barcodeidentifier)subfolder,intheoutputpathfolder.

Intensitydata(*.idat)filesareonlycreatedforsamplesthathave100%oftheirstripes

scanned.Thesefilesarenotcreatedwhenscanning

individualstripeswithinasample

sectiononaBeadChip.

Ifoneormorestripesfailscanningorregistrationinasamplesection,thestripescanbe

rescannedfromtheICSReviewscreenusingtheRescanbutton.Uponrescan,new

intensitydatafileswillbegenerated.

IfyouclickDoneontheICSReviewscreenwithoutrescanningthefailedsections,the

*.idatfileswillbecreatedwithoutdatafromthefailedsection,whichcouldreduceassay

performanceorresults.Theentiresamplesectionwillhavetoberescannedduringa

futuresessioninordertogeneratecomplete*.idatfiles.

WhenfailedsectionsonaBeadChipareimmediatelyrescannedwithinthecu rrentscan

session,newimagefileswillbecreatedonlyforthesectionsthatarescanned.Whenan

entireBeadChipisrescanned,allimagefilesarerecreated.

Newmetricsand*.idat/*.gtcand*.qcfilesarecreatedwitheachrescanand

overwrite

existingfiles.Ifyoudonotwantthistooccur,savetherescandatainanotheroutputdata

folder.

TheEffective.cfgfileisalsocreatedatthestartofascan andplacedintheArrayIDfolder

intheoutputpath.Itcontainsallofthescannerconfigurationinformation

forthatscan.

TheiScanReaderusesthisfilewhenscanningBeadChips.

NOTE

An*.idatfileis generatedwhentheregistrationdataforallstripesis

presentforagivensample.Ifallstripesarescanned,regardlessoftheir

resultsforregistrationorothermetrics,an*.idatfilewillalwaysbe

generated.Ifahardwareerroroccurswherebyatleastonestripein

the

sampleisnotscanned,thenno*.idatfilewillbegeneratedforthe

sample.

NOTE

Registrationandextractionarecriticaltoobtainingresultsfromyour

experiments.