Very low (negative) values in readcounts, copynumbers, copynumbersnormalized dataframes

[alexvasilikop]

Hello,

I have noticed that the software produced some very negative values for some bins. The issue starts from the readcounts and is propagated to the rest of the data (copynumbers etc). How can such values be produced? Even if there are 0 reads shouldn't these values be 0? Thanks a lot. Specifcally I am trying to find out why some parts of the Y chromosome is consistently lost across samples

Readcounts
Y:17200001-17300000 Y 17200001  17300000  6.129
Y:17300001-17400000 Y 17300001  17400000  5.907
Y:17400001-17500000 Y 17400001  17500000  5.524
Y:17500001-17600000 Y 17500001  17600000  1
Y:17600001-17700000 Y 17600001  17700000  -1022
Y:17700001-17800000 Y 17700001  17800000  -1022
Y:17800001-17900000 Y 17800001  17900000  -1022
Y:17900001-18000000 Y 17900001  18000000  -1022
Y:18000001-18100000 Y 18000001  18100000  -1022
Y:18100001-18200000 Y 18100001  18200000  -1022
Y:18200001-18300000 Y 18200001  18300000  1
Y:18300001-18400000 Y 18300001  18400000  -1022
Y:18400001-18500000 Y 18400001  18500000  -1022
Y:18500001-18600000 Y 18500001  18600000  -1022
Y:18600001-18700000 Y 18600001  18700000  4
Y:18700001-18800000 Y 18700001  18800000  1
Y:18800001-18900000 Y 18800001  18900000  4.322
Y:18900001-19000000 Y 18900001  19000000  5.585
Y:19000001-19100000 Y 19000001  19100000  6.129

Copy numbers
Y:17300001-17400000 Y 17300001  17400000  -1.197
Y:17400001-17500000 Y 17400001  17500000  -0.891
Y:17500001-17600000 Y 17500001  17600000  -4.454
Y:17600001-17700000 Y 17600001  17700000  -1022
Y:17700001-17800000 Y 17700001  17800000  -1022
Y:17800001-17900000 Y 17800001  17900000  -1022
Y:17900001-18000000 Y 17900001  18000000  -1022
Y:18000001-18100000 Y 18000001  18100000  -1022
Y:18100001-18200000 Y 18100001  18200000  -1022
Y:18200001-18300000 Y 18200001  18300000  -4.369
Y:18300001-18400000 Y 18300001  18400000  -1022
Y:18400001-18500000 Y 18400001  18500000  -1022
Y:18500001-18600000 Y 18500001  18600000  -1022
Y:18600001-18700000 Y 18600001  18700000  -2.716
Y:18700001-18800000 Y 18700001  18800000  -4.501
Y:18800001-18900000 Y 18800001  18900000  -1.594
Y:18900001-19000000 Y 18900001  19000000  -1.566

[alexvasilikop]

I realized this may come form the logTransform export of log(0). Any workaround?