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hyunhwan-jeong / CB2

CB2 is an R package which provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis. Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.
https://cran.r-project.org/web/packages/CB2/index.html
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gene_stat cpms #8

Closed AMChalkie closed 4 years ago

AMChalkie commented 4 years ago

Hi,

I've come across a case with confusing results:

At the gene_stat level, we sometimes get cpm_a < cpm_b, while logFC is -ve. It's to do with the combining of the replicates, but I think it would be useful to have information on the gene level of how many probes are consistent (in this case 3 or 4, or perhaps number_sgrna_up, number_sgrna_down?

Thanks Alistair

Gene level: n_sgrna cpm_a cpm_b logFC 4 10.20239 28.36188 -1.069289

sgrna level n_a n_b phat_a vhat_a phat_b vhat_b cpm_a cpm_b logFC 1 1 1.461569e-05 0 8.329479e-07 0 14.615689 0.83294789 -3.090759 1 1 1.686701e-05 0 1.114901e-04 0 16.867005 111.49007463 2.654428 1 1 5.288807e-06 0 8.329479e-08 0 5.288807 0.08329479 -2.537360 1 1 4.038075e-06 0 1.041185e-06 0 4.038075 1.04118486 -1.303466

hyunhwan-jeong commented 4 years ago

@AMChalkie thanks for the report, and our team also aware of that it is possible to have discrepancy between cpm and logFC. One of the plan is adding two modes for the logFC (averaged sgRNA-levels or directly from gene-level cpm). Regarding your number_sgrna_up and number_sgrna_down, Let me think about it.

Thank you,

Hyun-Hwan Jeong

hyunhwan-jeong commented 4 years ago

Duplicate of #9