edit vignettes/preprocessing

Author: Carol-seven

vignettes/preprocessing.qmd

@@ -66,7 +66,7 @@ and `PG.Quantity`. This function will reformat the data and provide
 functionality for some initial filtering (based on the number of unique peptides).
 The steps below describe the operations performed during preprocessing.
 
-**1\.** Loads the raw data
+### 1. Loads the raw data
 
 
 + If the raw data is in a `.csv` file
@@ -79,7 +79,7 @@ specify the `fileName` to read the raw data file into R.
 first load the data file directly, then specify the `dataSet` in the function.
 
 
-**2\.** Filters out identified proteins that exhibit `NaN` quantitative values
+### 2. Filters out identified proteins that contain no quantitative values (uncommon for Spectronaut-based results, can occur in MaxQuant-based results)
 
 
 `NaN`, which stands for "Not a Number," can be found in the `PG.Quantity` column
@@ -92,7 +92,7 @@ very similar or identical m/z values that lead to difficulty in parsing out
 individual intensity profiles.
 
 
-**3\.** Applies a unique peptides per protein filter
+### 3. Filters out proteins with < 2 unique peptide identifications
 
 
 General practice in the proteomics field is to filter out proteins which were
@@ -108,7 +108,7 @@ and we can help you evaluate the evidence from the raw data to determine
 believability.
 
 
-**4\.** Adds accession numbers to identified proteins without informative names
+### 4. Adds accession numbers to identified proteins without informative names
 
 
 Spectronaut reports contain 4 different columns of identifying information:
@@ -150,8 +150,7 @@ which is used in [PMF](https://proteomics.uconn.edu/) for most Scaffold-based
 results, do rank protein cluster IDs by likelihood of correctness). </div>
 
 
-**5\.** Saves a document to your working directory with all filtered out data,
-if desired
+### 5. Saves a document to your working directory with all filtered out data, if desired
 
 
 If `saveRm = TRUE`, the data removed in step 2 (`preprocess_filterNaN.csv`) and