Highlighting reviews - documentation and readme links

CITATION

@@ -1 +1,2 @@
-FIXME: describe how to cite this lesson.
+O’Callaghan A, Robertson G, LLewellyn M, Becher H, Meynert A, Vallejos C, Ewing A. (2024). High dimensional statistics with R. https://github.com/
+carpentries-incubator/high-dimensional-stats-r.

README.md

@@ -2,21 +2,7 @@
 
 [![Create a Slack Account with us](https://img.shields.io/badge/Create_Slack_Account-The_Carpentries-071159.svg)](https://swc-slack-invite.herokuapp.com/)
 
-**Thanks for contributing to The Carpentries Incubator!**
-This repository provides a blank starting point for lessons to be developed
-here.
-
-A member of the [Carpentries Curriculum Team](https://carpentries.org/team/)
-will work with you to get your lesson listed on the
-[Community Developed Lessons page][community-lessons]
-and make sure you have everything you need to begin developing your new lesson.
-
-## What to do next
-
-Before you begin developing your new lesson,
-here are a few things we recommend you do:
-
-* [ ] [Add relevant topic tags to your lesson repository][cdh-topic-tags].
+This repository is part of The Carpentries Incubator, a place for The Carpentries community to collaboratively create, test, and improve lessons.
 
 ## Contributing
 
@@ -42,6 +28,10 @@ Look for the tag
 This indicates that the maintainers will welcome a pull request fixing this
 issue.
 
+## Reviews
+
+The lesson has been iteratively developed and improved. For information on the development process, reviews and feedback from instructors following teaching see [REVIEWS](reviews.md).
+
 ## Maintainer(s)
 
 Current maintainers of this lesson are

_episodes_rmd/05-factor-analysis.Rmd

@@ -80,29 +80,10 @@ components are ordered by the amount of variance they account for.
 
 # Prostate cancer patient data
 
-The prostate dataset represents data from 97 men who have prostate cancer.
-The data come from a study which examined the correlation between the level
-of prostate specific antigen and a number of clinical measures in men who were
-about to receive a radical prostatectomy. The data have 97 rows and 9 columns.
+We revisit the prostate dataset of 97 men who have prostate cancer.
 Although not strictly a high-dimensional dataset, as with other episodes,
 we use this dataset to explore the method.
 
-
-Columns are:
-
-
-- `lcavol`: log (cancer volume)
-- `lweight`: log (prostate weight)
-- `age`: age (years)
-- `lbph`: log (benign prostatic hyperplasia amount)
-- `svi`: seminal vesicle invasion
-- `lcp`: log (capsular penetration); amount of spread of cancer in outer walls
-  of prostate
-- `gleason`: [Gleason score](https://en.wikipedia.org/wiki/Gleason_grading_system)
-- `pgg45`: percentage Gleason scores 4 or 5
-- `lpsa`: log (prostate specific antigen)
-
-
 In this example, we use the clinical variables to identify factors representing
 various clinical variables from prostate cancer patients. Two principal
 components have already been identified as explaining a large proportion

_extras/data.md

@@ -0,0 +1,88 @@
+---
+title: "Data"
+---
+
+# Prostate cancer data 
+[Source](https://search.r-project.org/CRAN/refmans/bayesQR/html/Prostate.html)
+
+Prostate specific antigen values and clinical measures for 97 patients hospitalised for a radical prostatectomy. Prostate specimens underwent histological and morphometric analysis. The column names refer to 
+
+- lcavol: log(cancer volume)
+- lweight: log(prostate weight)
+- age: age
+- lbph: log(benign prostatic hyperplasia amount)
+- svi: seminal vesicle invasion
+- lcp: log(capsular penetration)
+- gleason: Gleason score
+- pgg45: percentage Gleason scores 4 or 5
+- lpsa: log(prostate specific antigen)
+
+# Methylation data
+
+[Source](https://bioconductor.org/packages/release/data/experiment/html/FlowSorted.Blood.EPIC.html)
+
+Illumina Human Methylation data from EPIC on sorted peripheral adult blood cell populations. The data record DNA methylation assays for each individual, which measure, for many sites in the genome, the proportion of DNA that carries a methyl mark (a chemical modification that does not alter the DNA sequence). The methylation assays are recorded as normalised methylation levels (M-values), where negative values correspond to unmethylated DNA and positive values correspond to methylated DNA. The data object also contains phenotypic metadata for each individual such as age and BMI. Precisely, the data object contains: 
+
+- assay(data): normalised methylation levels 
+- colData(data): individual-level information
+    - Sample_Well: sample well
+    - Sample_Name: name of sample
+    - purity: sample cell purity 
+    - Sex: sex 
+    - Age: age in years
+    - weight_kg: weight in kilograms
+    - height_m: height in metres
+    - bmi: BMI
+    - bmi_clas: BMI class
+    - Ethnicity_wide: ethnicity, wide class
+    - Ethnic_self: ethnicity, self-identified
+    - smoker: yes/no indicator of smoker status
+    - Array: type of array from the EPIC array library
+    - Slide: slide identifier
+
+# Horvath data
+
+[Source](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0014821#s5)
+
+Methylation markers across different age groups. The CpGmarker variable used in this lesson are CpG site encodings.
+
+# Breast cancer gene expression data
+
+[Source](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2990)
+
+Gene expression data showing microarray results for different probes used to examine gene expression profiles in 91 different breast cancer patient samples and metdata for the sampled patients.
+
+- assay(data): gene expression data for each individual
+- colData(data): individual-level information
+  - Study: study identifier 
+  - Age: age in years
+  - Distant.RFS: indicator of distant relapse free survival  
+  - ER: estrogen receptor positive or negative status
+  - GGI: gene expression grade index 
+  - Grade: histologic grade 
+  - Size: tumour size in cm
+  - Time.RFS: time between the date of surgery and diagnosis of relapse (time in relapse free survival, RFS)
+
+# Single-cell RNA sequencing data
+
+[Source](https://pubmed.ncbi.nlm.nih.gov/25700174/)
+
+Gene expression measurements for over 9000 genes in over 3000 mouse cortex and hippocampus cells. These data are an excerpt of the original source.
+
+- assay(data): gene expression data 
+- colData(data): individual cell-level information
+  - tissue: tissue type
+  - group #: group number
+  - total mRNA mol: total number of observed mRNA molecules corresponding to this cell's unique barcode identifier
+    - well: the well that this cell's cDNA was stored in during processing
+  - sex: sex of the donor animal
+  - age: age of the donor animal 
+  - diameter: estimated cell diameter
+  - cell_id: cell identifier 
+  - level1class: a cluster label identified using a mix of computational techniques and manual annotation
+  - level2class: a cluster label identified using a mix of computational techniques and manual annotation
+  - sizeFactor:   estimate size factor calculated for scaling normalisation using (e.g., **`scran`**).
+
+
+{% include links.md %}
+

reference.md

@@ -2,7 +2,6 @@
 layout: reference
 ---
 
-## Glossary
 
 
 {% include links.md %}