User guide

72 Part # 11313539 Rev. B
Troubleshooting
Auto‐tiltpeaksdonotappearonthealignscreen
Sectionsmaybebrokenor
dirty.
EjecttheBeadChipsandvisuallyinspectsectionsto
ensurethatnonearebrokenordirty.Followlab
protocolsforcleaningsections,andreportbroken
sectionstotheresponsiblescientist.Tryscanningthe
BeadChipagain.
Lowintensityorpoor‐
performingsamples.
Reviewscanmetricstouncoverpotential
issues.
Stripeturnsredinsteadof
green.
Oneofthefourswathswithinthestripeisnotbeing
imagedcorrectly.Theswathmightbeoutoffocusorthe
BeadChipmightbemisaligned.Checktoensureproper
focusandBeadChipalignment.
Cause Resolution
BeadChipsdonotlieflat
withinthecarrier.
RemovetheBeadChipcarrierfromtheiScanReader
trayandreseattheBeadChips.Ensurethattheylie
completelyflatwithintheslotsonthecarrier.See
Chapter3,LoadingBeadChips.
The*.sdffilechosendoes
notmatchtheBeadChip
type.
Verifythatthe*.sdffileselectedmatchestheBeadChip
type.Ifitdoesnot,
thenrescantheBeadChipusingthe
correct*.sdffile.
Camerahastimedout. Power‐cyclethePCandscanner.
Cause Resolution