diff --git a/tex/thesis.tex b/tex/thesis.tex index ba1e9fc..9921fa9 100644 --- a/tex/thesis.tex +++ b/tex/thesis.tex @@ -100,6 +100,8 @@ \newacronym{moi}{MOI}{multiplicity of infection} \newacronym{ifng}{IFN$\upgamma$}{interferon-$\upgamma$} \newacronym{tnfa}{TNF$\upalpha$}{tumor necrosis factor-$\upalpha$} +\newacronym{sql}{SQL}{structured query language} +\newacronym{fcs}{FCS}{flow cytometry standard} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % SI units for uber nerds @@ -1056,6 +1058,34 @@ via a Biorad Bioplex 200 plate reader. \input{../tables/luminex_panel.tex} \end{table} +\subsection{data aggregation and meta-analysis} + +In order to perform meta-analysis on all experimental data generate using the +\gls{dms} system, we developed a program to curate and aggregate the raw +datafiles into a \gls{sql} database. + +% FIGURE summarize this stuff in a picture + +The data files to be aggregated included Microsoft Excel files which held +timeseries measurements for cell cultures (eg cell counts, viability, glucose, +\gls{il2} added, media added, and media removed), \gls{fcs} files for cellular +phenotypes, and FlowJo files which held gating parameters and statistics based +on the \gls{fcs} files. Additional information which was held in electronic lab +notebooks (eg OneNote files) was not easily parsable, and thus this data was +summarized in YAML files. The data included in these YAML files included reagent +characteristics (vendor, catalog number, lot number, manufacturing date), cell +donor characteristics (age, \gls{bmi}, phenotype, demographic, gender), and all +experimental parameters such as the number of bead or \gls{dms} added. + +% FIGURE data model + +To aggregate the data in a database, we wrote a program using Python, R, and +Docker which retrieved the data from its source location and inserted the data +in a Postgres database. This program included checks to ensure the integrity of +source data (for example, flagging entries which had a reagent whose +manufacturing date was after the date the experiment started, which signifies a +human input error). + \subsection{statistical analysis} For 1-way \gls{anova} analysis with Tukey multiple comparisons test, @@ -1077,9 +1107,6 @@ lack-of-fit tests where replicates were present (to assess model fit in the context of pure error). Statistical significance was evaluated at $\upalpha$ = 0.05. -% METHOD add meta-analysis -% METHOD add Grex - \section{results} \subsection{DMSs can be fabricated in a controlled manner}