06/23/2020 Resources: Slides: https://www.synapse.org/#!Synapse:syn22213391 https://www.synapse.org/#!Synapse:syn22149791/wiki/603821 (scroll down) Lecture Recording: https://www.synapse.org/#!Synapse:syn22149791/wiki/603802 In the future we aim to post resources a few hours after the lesson finishes.

Created by Xengie Doan xengie.doan
@kharold The system is open to accept module1's solutions and variable names have been updated in the submission helpers. Please rerun lines 10-15 and use my_gene, my_delta, my_description, and my_rationale variables in the notebook to submit answers. Thanks!
Thanks for the sleuthing @kharold , we also realized that after you brought it up! @mnikolov will update the variable name and it should work after that.
@xengie.doan ```{r} my_gene <- "PEG10" my_delta <- my_logtpm_df["PEG10", "delta"] ``` Here's my code for that section... The given variable name was my_gene, not my_gene_id. I also noticed that the submission (in the submission helpers file) submits the variables my_gene_id, my_element, and my_gene_name, none of which are initialized in the activity... There is my_gene, my_delta, my_description, and my_rationale.
@kharold Hi! Could you share the code you used when you chose a gene ID? if you could copy paste in into the comment as a "Code Block" that would be great! It sounds like you didn't assign my_gene_id a gene ID from the error.
Hi! I finished the questions for Module 1, but it returns an error when I tried to submit it (object my_gene_id not found). Any help would be greatly appreciated! P.S. Other than that, I had a lot of fun working on this activity!
Hi @jcortez1 ! Thanks for asking a question on the discussion. Feel free to make a new thread for a new topic in the future. For your first question: I'd suggest you refer to lines 263 to 283, which is the same analysis but for Breast Cancer. You are correct that the "hyal_col_df" dataframe contains motility data (speed_um_hr) so you need to use a different dataframe with expression data. To see how the motility information and expression data line up in different dataframes, refer to lines 191-193. For your second question : In line 320 ``` my_logtpm_df$delta <- ... # fill in here ``` creates a new column named delta for you, so you are correct that it does not already exist. Tagging @agsynapse if there is anything else
Xengie and/or Milen, I had a question regarding the second question on Module 1. What column do you mean when you're asking for the "expression values" between the two (colon) cancer lines? Unless I messed up, I don't see any column with that name - I have a data frame that is 2x21. However, I do see a column that says "average_value_scaled". Are you referencing this or something else? Everything seems to be in reference to the speed_um_hr, which is confusing me. Additionally, for #3, when it says "store in the 'delta' column," I don't see a delta column. Should I create one or am I once again missing something? I think I should be using the same data frame.

Announcement: Module 1 Resources Uploaded page is loading…