Merge pull request #15 from 3mmaRand/fix-omics-2

Fix omics 2
3mmaRand · Oct 19, 2023 · 74ff924 · 74ff924
2 parents 4a7dd22 + 0bc3400
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diff --git a/omics/week-3/workshop.qmd b/omics/week-3/workshop.qmd
@@ -63,7 +63,7 @@ These are the three datasets. Each set compromises several files.
 -   [xlaevis_counts_S14.csv](data-raw/xlaevis_counts_S14.csv)
 -   [xlaevis_counts_S20.csv](data-raw/xlaevis_counts_S20.csv)
 -   [xlaevis_counts_S30.csv](data-raw/xlaevis_counts_S30.csv)
--   [meta_data.txt](data-raw/meta_data.txt)
+
 
 🐭 Stem cell data:
 

diff --git a/omics/week-4/workshop.qmd b/omics/week-4/workshop.qmd
@@ -523,6 +523,8 @@ prog_hspc |>
 
 ```
 
+Notice that we have summed across all the columns.
+
 ❓ What do you conclude?
 
 <!-- #---THINKING ANSWER--- -->
@@ -552,7 +554,7 @@ rowSums(prog_hspc) |> sort() |> head(10)
 To find the genes that are expressed in only one cell type, we can use
 the same approach as above but only sum the columns for one cell type.
 
-🎬 Find the genes that are 0 in every column for the Prog cells:
+🎬 Find the genes that are 0 in every column for the HSPC cells:
 
 ```{r}
 prog_hspc |> 
@@ -561,18 +563,21 @@ prog_hspc |>
 
 ```
 
+We have summed across the HSPC cells only. 
 Note that if we knew there were some rows that were all zero across both
-cerll types, we would need to add
+cell types, we would need to add
 `|> filter(sum(c_across(Prog_001:Prog_852)) != 0)`
 
-🎬 Now you find the genes that are 0 in every column for the HSPC cells:
+meaning zero in all the HSPC but not zero in all the Prog
+
+🎬 Now you find the genes that are 0 in every column for the Prog cells:
 
 ```{r}
 #| echo: false
 #---CODING ANSWER---
 prog_hspc |> 
   rowwise() |> 
-  filter(sum(c_across(HSPC_001:HSPC_852)) == 0)
+  filter(sum(c_across(Prog_001:Prog_852)) == 0)
 
 ```
 
@@ -694,7 +699,7 @@ practical. Qmd stands for Quarto markdown. It allows code and ordinary
 text to be interleaved to produce well-formatted reports including
 webpages. Right-click on the link and choose Save-As to download. You
 will be able to open the Qmd file in RStudio. Alternatively, [View in
-Browser](https://github.com/3mmaRand/). Coding and thinking answers are
+Browser](https://github.com/3mmaRand/BIO00088H-data/blob/main/omics/week-4/workshop.qmd). Coding and thinking answers are
 marked with `#---CODING ANSWER---` and `#---THINKING ANSWER---`
 
 Pages made with R [@R-core], Quarto [@allaire2022], `knitr` [@knitr],

diff --git a/omics/week-5/data-processed/hspc_summary_gene.csv b/omics/week-5/data-processed/hspc_summary_gene.csv
diff --git a/omics/week-5/data-processed/hspc_summary_samp.csv b/omics/week-5/data-processed/hspc_summary_samp.csv
diff --git a/omics/week-5/data-processed/prog_summary_gene.csv b/omics/week-5/data-processed/prog_summary_gene.csv
diff --git a/omics/week-5/data-processed/prog_summary_samp.csv b/omics/week-5/data-processed/prog_summary_samp.csv