CRISPR screen 0 count values

Question

[morovatunc]

Hi,

I would like to calculate simple log fold change between two conditions. However, I have 0 values which makes the calculation problematic. I have 4 sgRNA for a gene, counts refer to their values.

The problem is, I am ok with dealing the rows which have all zeros. But the problem is with the rows which have both. Therefore, I have concerns about what should be my method.

Any help would be appreciated,

Best,

Tunc.

[jotan]

Could you post an example of what the data looks like with the problem lines?

Would adding a small value to all the raw data (e.g. x+0.001) help with the log transformations?

[morovatunc]

Dear Jotan thank you for your answer.

I solved the problem by adding +1 to all of the cells. Then take the ratio of two conditions. After that I took the log2.

My problem was like;

sampleA sampleB sample C
guide1 0 0 39
guide2 103 0 31
guide3 0 0 0