Minor updates to text

Makerere_Course_Materials/04_DE_analysis_with_DESeq2.Rmd

@@ -36,6 +36,13 @@ txi <- readRDS("RObjects/txi.rds")
 sampleinfo <- read_tsv("data/samplesheet_corrected.tsv", col_types = "cccc")
 ```
 
+First check the metadata.
+
+```{r}
+sampleinfo
+```
+
+
 It is important to be sure that the order of the samples in rows in the sample 
 meta data table matches the order of the columns in the data matrix - `DESeq2`
 will **not** check this. If the order does not match you will not be running the
@@ -261,14 +268,13 @@ The default significance level for independent filtering is `0.1`, however, you
 should set this to the FDR cut off you are planning to use. We will use `0.05` -
 this was the purpose of the `alpha` argument in the previous command.
 
-Remember 
-in Session 7 we said that there is no need to pre-filter the genes as DESeq2
-will do this through a process it calls 'independent filtering'. The genes 
-with `NA` are the ones `DESeq2` has filtered out.
+Earlier we said that there it is not necessary to carefully to pre-filter the
+genes as DESeq2 will do this through a process it calls 'independent filtering'.
+The genes with `NA` are the ones `DESeq2` has filtered out.
 
 ## Fitting an additive model
 
-So far we have fitted a simple model considering just "Status", but in reality 
+So far we have fit a simple model considering just "Status", but in reality 
 we want to model the effects of both "Status" and "Time Point".
 
 Let's start with the model with only main effects - an additive model with no 
@@ -288,6 +294,13 @@ results.additive <- results(ddsObj, alpha = 0.05)
 
 ### The default contrast of `results`
 
+Let's look at the results.
+
+```{r}
+results.additive
+```
+
+
 The `results` function has returned the results for the contrast "Infected vs
 Uninfected". Let's have a look at the model matrix to understand why `DESeq2`
 has given us this particular contrast.
@@ -332,7 +345,7 @@ resultsNames(ddsObj)
 
 ```{r}
 results.d33vd11 <- results(ddsObj, name = "TimePoint_d33_vs_d11", alpha = 0.05)
-
+results.d33vd11
 sum(results.d33vd11$padj < 0.05, na.rm = TRUE)
 ```