How to handle “weirld characters” in signal intensity files?
Sometimes, Illumina BeadStudio/Genome studio may export signal intensity values with weird characters. This could occur in non-English version of BeadStudio, in non-English version of Windows, in non-human SNP arrays, or any other reasons. For example, the LRR values for several markers in a file may display as “ABCDE” rather than a number, and PennCNV will ignore these values and ignore these markers in analysis. If they are “-inf” instead, PennCNV will treat them as -5. This should usually affect only a few markers for each sample. But some other times, all the signal intensity values are wrong so PennCNV will not work at all. For example, all the decimal points in LRR/BAF become “comma”, so they are not valid numbers. In that case, users can do “perl -pe ‘s/,/./g’ < inputfile > outputfile” to generate a new signal intensity file for CNV calling.
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