# Conflicting values in CN data

**URL:** <https://forum.depmap.org/t/conflicting-values-in-cn-data/3909>\
**Category:** Issues and Bugs\
**Created:** [January 15, 2025, 8:44pm UTC](https://forum.depmap.org/t/conflicting-values-in-cn-data/3909 "2025-01-15T20:44:55Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![cwright1](https://avatars.discourse-cdn.com/v4/letter/c/e9bcb4/32.png) [@cwright1](https://forum.depmap.org/u/cwright1)\
**Post date:** [January 15, 2025, 8:44pm UTC](https://forum.depmap.org/t/conflicting-values-in-cn-data/3909/1 "2025-01-15T20:44:55Z")

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Using `Copy Number Public 24Q4` data, shouldn’t these be the linear (non-log-transformed) versions of `Copy Number Public 24Q4 (Log2 transformed)` ?

I’ve loaded both linear and log2-transformed data in toy data frames called `test1` and `test2`, respectively.

Some values agree, like `MYCN` in the cell line `KELLY`:

```auto
> test1 %>% filter(cell_line_display_name=="KELLY") %>% pull("MYCN")
[1] 232.3561

> test2 %>% filter(cell_line_display_name=="KELLY") %>% pull("MYCN")
[1] 7.86639

#Checks out
> log2(232.3561)
[1] 7.860194

```

But others **do not** agree, like `MYCN` in `CHLA90`

```auto
> test1 %>% filter(cell_line_display_name=="CHLA90") %>% pull("MYCN")
[1] 1.413915

> test2 %>% filter(cell_line_display_name=="CHLA90") %>% pull("MYCN")
[1] 1.271375

#Obviously wrong
> log2(1.413)
[1] 0.4987615

```

I don’t know which value in which gene/cell line is correct.

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**Author:** ![simz](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/simz/32/440_2.png) [@simz](https://forum.depmap.org/u/simz)\
**Post date:** [January 15, 2025, 10:13pm UTC](https://forum.depmap.org/t/conflicting-values-in-cn-data/3909/2 "2025-01-15T22:13:37Z")

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Hi,

`Copy Number Public 24Q4 (Log2 transformed)` is in fact log2(CN + 1). If you add the pseudocount to the equation, the numbers should line up.

Best,  
Simone