Help with downstream analyses when running rnascope_mouse.m

[Sofiemb]

Hi,

I am trying to run the Mouse RNAscope workflow as described in mouse_vignette.md.

I managed to run the entire script and have now the two files: long_data.csv and man.csv but have problems understanding the downstream analyses.

A dataframe from long_data.csv for channel 1 (BdnfEx4) is shown in the guide but I am confused were to find these values in the long_data.csv file.

Is no_of_dots_c1 = D_c1 in long_data.csv, and avg_dot_size_c1 = V_c1 in long_data.csv, and avg_dot_Intensity_c1 = MI_D_c1 in long_data.csv?

Best regards,

Sofie

[andrewejaffe]

please see: https://github.com/LieberInstitute/dotdotdot/blob/master/docs/mouse_vignette.md#description-of-output

[Sofiemb]

Thanks for the link.

I am just confused how you made this table from the long_data file? I can not find the same values as shown here:

Thanks for the help,

Sofie

[andrewejaffe]

yeah, that example I guess had old naming...your interpretation in your original issue is correct

On Tue, Oct 6, 2020 at 9:50 AM Sofiemb notifications@github.com wrote:

Thanks for the link.

I am just confused how you made this table from the long_data file? I can not find the same values as shown here:

[image: Udklip] https://user-images.githubusercontent.com/72393726/95209640-e32c3900-07ea-11eb-9faf-5134031cb341.PNG

Thanks for the help,

Sofie

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[Sofiemb]

Thanks! :)