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niaid / dsb

Normalize CITEseq Data
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object 'count_prot' not found #25

Closed johaab closed 3 years ago

johaab commented 3 years ago

Hi! I was trying to run your vignette and the code fails at Step III (option b) because "count_prot" hasn't been defined anywhere. Could you please indicate what this variable corresponds to exactly and maybe update your vignette?

MattPM commented 3 years ago

Hi @johaab thanks for finding that, count_prot should be the raw protein counts x cells data which is cells_mtx_rawprot defined earlier in the vignette. That section is just making an object of the raw protein x cells data to define an Altexp object which then the dsb normalized data are added to.

I'll be updating the vignette in the next couple days to include some points discussed here :https://github.com/niaid/dsb/issues/20 and will add this.

thanks!

MattPM commented 3 years ago

Please see the updated documentation on the main github readme. (documentation will be updated on CRAN as well soon).