Fix some nomenclature errors

abbrevs.tex

@@ -13,9 +13,10 @@
 \newabbreviation{PCoA}{PCoA}{principal coordinate analysis} % AKA MDS?
 \newabbreviation{MOFA}{MOFA}{Multi-Omics Factor Analysis}
 \newabbreviation{LF}{LF}{latent factor}
-\newabbreviation{logCPM}{logCPM}{$\log_2$ counts per million}
+%% Note: Can't start with math or else capitalization fails
+\newabbreviation{logCPM}{logCPM}{log$_2$ counts per million}
 \newabbreviation{CPM}{CPM}{counts per million}
-\newabbreviation{logFC}{logFC}{$\log_2$ fold change}
+\newabbreviation{logFC}{logFC}{log$_2$ fold change}
 \newabbreviation{RMA}{RMA}{Robust Multichip Average}
 \newabbreviation{fRMA}{fRMA}{frozen Robust Multichip Average}
 \newabbreviation{GRSN}{GRSN}{Global Rank-invariant Set Normalization}

thesis.lyx

@@ -17547,19 +17547,6 @@ RNA-seq
 Normalization and Exploratory Data Analysis
 \end_layout
 
-\begin_layout Standard
-\begin_inset Flex TODO Note (inline)
-status open
-
-\begin_layout Plain Layout
-This paragraph is throwing LaTeX errors.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
 \begin_layout Standard
 Libraries were normalized by computing scaling factors using the 
 \begin_inset Flex Code
@@ -17590,15 +17577,12 @@ literal "false"
 \end_inset
 
 .
- HELLO 
-\begin_inset ERT
+ 
+\begin_inset Flex Glossary Term (Capital)
 status open
 
 \begin_layout Plain Layout
-
-
-\backslash
-gls*{logCPM}
+logCPM
 \end_layout
 
 \end_inset
@@ -17788,7 +17772,7 @@ GB
 
 \end_inset
 
- and SampleID.
+ and Sample ID.
  To test the effect of 
 \begin_inset Flex Glossary Term
 status open
@@ -18653,19 +18637,10 @@ literal "false"
 \begin_inset Flex Glossary Term
 status open
 
-\begin_layout Plain Layout
-\begin_inset Flex Glossary Term
-status open
-
 \begin_layout Plain Layout
 GB
 \end_layout
 
-\end_inset
-
-
-\end_layout
-
 \end_inset
 
  cuts the required sequencing effort (and costs) to achieve a target coverage