User guide

52 Part # 11313539 Rev. B
Viewing Scan Results
Scan M etrics
ThescanmetricsforeachBeadChipappearintheScanMetricstableatthetopofthe
Reviewscreen.Thistableallowsyoutoreviewintensityvaluesinboththeredandgreen
channels,checktheregistrationandfocusmetricsforeachstripeontheBeadChip,and
determinewhetherintensitydata
wasnormalizedforeachBeadChipsectionthatwas
scanned.
` Thefocusmetricrangesbetween0and1.Thehigherthefocusscore,thesharperand
morewell‐definedthebeadimageswillbe,leadingtohighbeadintensityvalues.A
lowfocusscoremeansthatthebeadimagesarenotwelldefined(beadcolorswill
bleedintoeachotheron
images),causingbeadintensityvaluestodecrease.
` TheregistrationvaluevariesdependingonthetypeofBeadChip,rangingbetween0
and1(multipleswathsperarray)orbetween0and2(singleswathperarray).When
thestriperegistrationislessthan0.75,thestripegetsmarkedasmisregisteredandis
coloredredintheScanProgressIndicator
window.Misregisteredsectionscanbe
rescanned.See
CompletingaScanonpage47.
` ThenormalizationmetricisshownintheAutoConvertcol umnandisoneofthe
followingforeachBeadChipsectionthatwasscanned:
• Converted—ICSconvertedthe*.idatfileforthatBeadChipsectiontoa*.gtcfile
afterthesectionwasscanned(theintensitydatawasnormalizedandgenotype
callsweregenerated).(See
GeneratedFilesonpage57.)
• N/A—TheAutoConvertfeaturewasnotenabledforthisscan.(SeeGenerating
NormalizedDataandGenotypeCallsonpage37.)
• NotConverted—TheAutoConvertfeaturewasenabledforthisscan,butthe
*.idatfileforthatBeadChipsectionwasnotconvert edtoa*.gtcfile.To
troubleshoot,see
LogFilesonpage51.
Scanmetricsarealsostoredintwotextfil es,Metrics.txtand[Barcode]_qc.txt,where
[Barcode]representsthebarcodenumberforasingleBeadChip.
Figure36Contentsofa[Barcode]_qc.txtScanMetricsFile