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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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Warning when running normalize_affy_geno_cluster.pl #57

Open hannanw opened 4 years ago

hannanw commented 4 years ago

Hi, 

I am new to microarrays and have little experience in processing them. Sorry if the issues seems naive. When i generate the LRR and BAF values using normalize_affy_geno_cluster.pl it seems like I get a warning for each file that the R_expected < 0 e.g. WARNING: R_expected < 0 due to rmean=6403.7274 6403.7274 2436.2669 thetamean=0.0520 0.2613 0.4705 a=1163.21333654269 b=2509.26652278459 r=3672.47985932728 theta=0.723656832770997. There are multiple such errors every time I try to generate the LRR_BAF.txt
What does this warning mean and how do I go about correcting or rectifying it? Any help or pointers would be greatly appreciated.

Thanks, hannanw

michaelofrancis commented 4 months ago

Hi Hannaw, did you ever figure this out? I would also like clarity on this warning. Thanks!

kaichop commented 4 months ago

This is a warning message that can be ignored. Some markers do not have good clustering and thus yield such message.