class data info

3mmaRand · Feb 23, 2024 · 3925927 · 3925927
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diff --git a/r4babs4/week-4/study_before_workshop.qmd b/r4babs4/week-4/study_before_workshop.qmd
@@ -9,6 +9,7 @@ toc-location: right
    i.   Save your data files to the project.
    ii.  Go through the script and identify the parts that you need to change to make it work for your data.
    iii.  Can you identify code that you will not need to include?
-   iv.  Consider attempting to import and analyse your own data so that you can make good use of the workshop to resolve any issues you encounter.
+   iv.   Go through the [Week 2 Workshop](../week-2/workshop.html) and read the text to check you understand what is happening to the data.
+   v.  Consider attempting to import and analyse your own data so that you can make good use of the workshop to resolve any issues you encounter.
 
 
diff --git a/r4babs4/week-4/workshop.qmd b/r4babs4/week-4/workshop.qmd
@@ -33,23 +33,36 @@ In this workshop you will use the tools you used in the previous workshop (and b
 
 You need to provide the following information for the class dataset:
 
--    
+-   group_name:	A name for your group. Take care not to use a name used by others. Take care to use the exactly the same name for each of your rows
 
+-   cell_treatment:	One of MEDIA, LPS or ECOLIGreen
 
+-   antibody:	One of ISOTYPE or TNFAPC
 
+-   n_cells:	number of cells in sample after flowAI cleaning
 
-## How to change the name of an RStudio project.
+-   n_cells_live:	number of cells in sample after flowAI cleaning and removing debris
+
+-   perc_nondebris:	% "cleaned" cells that were not debris
+
+-   apc_cut:	threshold for logicle transformed TNFa_APC_Lin. This will be the same for all your samples
+
+-   apc_mfi:	Mean fluorescence intensity of the logicle transformed TNFa_APC_Lin in the TNF-α positive cells
 
-You can change the name of an RStudio project closing the project and renaming the project folder and the `.Rproj` file.
+-   n_pos_tnfa:	Number of TNF-α positive cells
 
+-   perc_tfna_pos:	% non debris cells that are TNF-α positive cells    
 
-## Look after future you!
+Enter these in the [BIO00066I Biomedical Sciences class data](https://docs.google.com/spreadsheets/d/104EXdgsiIq-FuRF9Ly9zewEVdpkVWbyOwxSAmiqJepg/edit#gid=0)
+
+
+## How to change the name of an RStudio project.
 
-......
+You may need to rename your RStudio Project to your exam number before you submit. You can change the name of an RStudio project by:
 
-You're finished!
+-   closing the project
 
-# 🥳 Well Done! 🎉
+-   renaming both the project folder and the `.Rproj` file.