logR and copy.number in cna.seg. files

[daguilarvhio]

Dear all,

I am struggling to understand some of the data in the *cna.seg files output, particularly how the "copy.number" column if derived from the "logR" column.

I understand that the copy number is calculated as:

No loss/gain= log2(2/2) = 0 One copy gain = log2(3/2) = 0.57 Two-copy gain = log2(4/2) = 1 One-copy loss = log2(1/2) = -1

(As mentioned earlier in this forum).

However, this is not what I see in the *cna.seg files output. For instance:

chr	start	end	copy.number	event	logR	subclone.status	Corrected_Copy_Number	Corrected_Call	logR_Copy_Number
6	28500001	29000000	5	HLAMP	-9.0929	0	5	HLAMP	0.015625
6	29000001	29500000	5	HLAMP	-10.0687	0	5	HLAMP	0.015625
6	29500001	30000000	5	HLAMP	-4.5952	0	5	HLAMP	0.015625
6	30000001	30500000	5	HLAMP	-10.031	0	5	HLAMP	0.015625
6	30500001	31000000	5	HLAMP	NA	0	5	HLAMP	NA
6	31000001	31500000	5	HLAMP	-7.8582	0	5	HLAMP	0.015625
6	31500001	32000000	5	HLAMP	NA	0	5	HLAMP	NA
6	32000001	32500000	5	HLAMP	NA	0	5	HLAMP	NA
6	32500001	33000000	5	HLAMP	-8.9581	0	5	HLAMP	0.015625
6	33000001	33500000	5	HLAMP	-3.2627	0	5	HLAMP	0.015625

How is it possible that a logR=-9.0929 generates to a copy.number=5?

Another example:

chr	start	end	copy.number	event	logR	subclone.status	Corrected_Copy_Number	Corrected_Call	logR_Copy_Number
4	500001	1000000	0	HOMD	-0.0322	0	0	HOMD	0.015625
4	1500001	2000000	0	HOMD	0.0093	0	0	HOMD	8.852849318524
4	2000001	2500000	0	HOMD	0.0695	0	0	HOMD	42.7650489610307

Shouldn't a logR ~0 mean that copy.number=2, instead of copy.number=0?

Am I missing something in the way that copy.number is calculated?

[SuqinYang]

@daguilarvhio Hi,have you solved the problem? This question confuses me too.