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\usepackage{seqsplit}           % Splits long words.
%\usepackage{opensans}          % Can't make this work so far. Shame. Would be lovely.
\usepackage[normalem]{ulem}     % For underlining links
% Most of the following are not required for the majority
% of cheat sheets but are needed for some symbol support.
\usepackage{amsmath}            % Symbols
\usepackage{MnSymbol}           % Symbols
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% Document Info
\author{Nimisha (lemonbuzz)}
\pdfinfo{
  /Title (microarray.pdf)
  /Creator (Cheatography)
  /Author (Nimisha (lemonbuzz))
  /Subject (Microarray Cheat Sheet)
}

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% Header and Footer
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\fancyhead[L]{
\noindent
\begin{multicols}{3}
\begin{tabulary}{5.8cm}{C}
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    \vspace{-7pt}
    {\parbox{\dimexpr\textwidth-2\fboxsep\relax}{\noindent
        \hspace*{-6pt}\includegraphics[width=5.8cm]{/web/www.cheatography.com/public/images/cheatography_logo.pdf}}
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\columnbreak
\begin{tabulary}{11cm}{L}
    \vspace{-2pt}\large{\bf{\textcolor{DarkBackground}{\textrm{Microarray Cheat Sheet}}}} \\
    \normalsize{by \textcolor{DarkBackground}{Nimisha (lemonbuzz)} via \textcolor{DarkBackground}{\uline{cheatography.com/132716/cs/40278/}}}
\end{tabulary}
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\fancyfoot[L]{ \footnotesize
\noindent
\begin{multicols}{3}
\begin{tabulary}{5.8cm}{LL}
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  \mymulticolumn{2}{p{5.377cm}}{\bf\textcolor{white}{Cheatographer}}  \\
  \vspace{-2pt}Nimisha (lemonbuzz) \\
  \uline{cheatography.com/lemonbuzz} \\
  \end{tabulary}
\vfill
\columnbreak
\begin{tabulary}{5.8cm}{L}
  \SetRowColor{FootBackground}
  \mymulticolumn{1}{p{5.377cm}}{\bf\textcolor{white}{Cheat Sheet}}  \\
   \vspace{-2pt}Published 13th September, 2023.\\
   Updated 16th September, 2023.\\
   Page {\thepage} of \pageref{LastPage}.
\end{tabulary}
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  \mymulticolumn{1}{p{5.377cm}}{\bf\textcolor{white}{Sponsor}}  \\
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  \vspace{-5pt}
  %\includegraphics[width=48px,height=48px]{dave.jpeg}
  Measure your website readability!\\
  www.readability-score.com
\end{tabulary}
\end{multicols}}




\begin{document}
\raggedright
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% Set font size to small. Switch to any value
% from this page to resize cheat sheet text:
% www.emerson.emory.edu/services/latex/latex_169.html
\footnotesize % Small font.

\begin{multicols*}{3}

\begin{tabularx}{5.377cm}{x{0.9954 cm} x{3.9816 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Introduction}}  \tn
% Row 0
\SetRowColor{LightBackground}
\seqsplit{Principle} & Amount of hybridisation detected is proportional to no. of fragments in sample \tn 
% Row Count 3 (+ 3)
% Row 1
\SetRowColor{white}
\seqsplit{Microarray} & DNA probes bound to glass slide, to which sample DNA fragments can be hybridised \tn 
% Row Count 6 (+ 3)
% Row 2
\SetRowColor{LightBackground}
Probes & Oligonucleotides, ink-jet printed onto slides (Agilent) or synthesised in-situ (Affymetrix) \tn 
% Row Count 9 (+ 3)
% Row 3
\SetRowColor{white}
Sample & labelled ssDNA or antisense RNA \tn 
% Row Count 10 (+ 1)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{1.64241 cm} x{3.33459 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Replicates}}  \tn
% Row 0
\SetRowColor{LightBackground}
Technical replicate & Repeated measurements or procedures using the same biological sample to evaluate precision and reproducibility \tn 
% Row Count 5 (+ 5)
% Row 1
\SetRowColor{white}
Biological replicate & Use of multiple independent biological samples to account for biological variability \tn 
% Row Count 9 (+ 4)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{2.04057 cm} x{2.93643 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{One and Two Color Arrays}}  \tn
% Row 0
\SetRowColor{LightBackground}
One Color Array \{\{width=30\}\} & Each sample loaded into a separate microarray \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
Two Color Array & Two samples, labelled differently, loaded onto same microarray in same amounts. \{\{nl\}\}Competitive hybridisation. \tn 
% Row Count 7 (+ 5)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{2.28942 cm} x{2.68758 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Data Preprocessing}}  \tn
% Row 0
\SetRowColor{LightBackground}
Background Correction \{\{width=30\}\} & - Adjust for non-specific hybridisation \{\{nl\}\} - mismatch probes (Affymetrix) \{\{nl\}\} - exogenous negative control spots \{\{nl\}\} - remove features with lower intensity than background \tn 
% Row Count 9 (+ 9)
% Row 1
\SetRowColor{white}
Log Transformation & Improves data distribution for classical statistical analysis \tn 
% Row Count 12 (+ 3)
% Row 2
\SetRowColor{LightBackground}
Normalisation & Removes systematic effects due to technical differences, which aren't due to biological differences \tn 
% Row Count 17 (+ 5)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{2.4885 cm} x{2.4885 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Normalisation}}  \tn
% Row 0
\SetRowColor{LightBackground}
WithinArray Normalisation \{\{width=30\}\} & Two-color microarrays; \{\{nl\}\} align two channels for each array \tn 
% Row Count 4 (+ 4)
% Row 1
\SetRowColor{white}
BetweenArray Normalisation & One-color microarrays; \{\{nl\}\}Single channel platforms; \{\{nl\}\} Quantile normalisation, Cyclic Loess \tn 
% Row Count 10 (+ 6)
% Row 2
\SetRowColor{LightBackground}
Sources of Bias & Dye bias, Array bias, Spatial bias \tn 
% Row Count 12 (+ 2)
% Row 3
\SetRowColor{white}
Dye Swap Design & pair of samples compared twice with reversed dye \tn 
% Row Count 15 (+ 3)
% Row 4
\SetRowColor{LightBackground}
Reference Design & Each sample hybridised against a common reference sample \tn 
% Row Count 18 (+ 3)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{2.4885 cm} x{2.4885 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Within Array Normalisation}}  \tn
% Row 0
\SetRowColor{LightBackground}
Sources of Bias \{\{width=30\}\} & - Differential dye incorporation \{\{nl\}\} - Diff. emission response to excitation \{\{nl\}\} - Non-uniform focusing across the array \tn 
% Row Count 7 (+ 7)
% Row 1
\SetRowColor{white}
Correction of diff responses of Cy3 and Cy5 channels & 1. LR of Cy3 vs Cy5 intensity \{\{nl\}\} 2. LR of log ratio against avg. intensity ({\bf{MA plot}}) \{\{nl\}\} 3. Non-linear ({\bf{Loess}}) regression of log ratio against avg. intensity \tn 
% Row Count 16 (+ 9)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
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\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{X}
\SetRowColor{DarkBackground}
\mymulticolumn{1}{x{5.377cm}}{\bf\textcolor{white}{MA plots}}  \tn
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\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{1.84149 cm} x{3.13551 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{MA plot - Interpretation}}  \tn
% Row 0
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Vertical axis & Log ratio (R/G) = M i.e. log fold change; \{\{nl\}\} M = log2 (condA exp / condB exp) \tn 
% Row Count 4 (+ 4)
% Row 1
\SetRowColor{white}
Horiontal axis & average log-intensity between two cond; \{\{nl\}\} mean(condA exp + condB exp) \tn 
% Row Count 7 (+ 3)
% Row 2
\SetRowColor{LightBackground}
Non-zero intercept & One channel is consistently brighter than the other \tn 
% Row Count 10 (+ 3)
% Row 3
\SetRowColor{white}
Slope not equal to 1 & One channel responds more strongly at high intensities than other \tn 
% Row Count 13 (+ 3)
% Row 4
\SetRowColor{LightBackground}
Slope not straight line & Non-linear relation b/w intensities of two channels \tn 
% Row Count 16 (+ 3)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
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\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{p{0.74655 cm} x{4.23045 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Loess Regression}}  \tn
% Row 0
\SetRowColor{LightBackground}
\seqsplit{Working} & - local reg in overlapping windows of data \{\{nl\}\} - join the regression to form a smooth curve \tn 
% Row Count 3 (+ 3)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
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\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{1.74195 cm} x{3.23505 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Between Array Normalisation}}  \tn
% Row 0
\SetRowColor{LightBackground}
Types & Scaling, centering, distribution normalisation \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
Scaling & Ensure mean/median of all distributions are equal; Subtract overall mean log intensity from each log intensity \tn 
% Row Count 7 (+ 5)
% Row 2
\SetRowColor{LightBackground}
Centering & Ensure that all the distribution's mean and SD are equal \tn 
% Row Count 10 (+ 3)
% Row 3
\SetRowColor{white}
Quantile normalisation & - sort each array in order \{\{nl\}\} - average across rows \{\{nl\}\} - sort avg values in original order \tn 
% Row Count 14 (+ 4)
% Row 4
\SetRowColor{LightBackground}
Explanatory variables & {\bf{Covariates}} (quantitative measurements) and {\bf{factors}} (categorical variables) \tn 
% Row Count 18 (+ 4)
% Row 5
\SetRowColor{white}
Levels & Unique values within a factor \tn 
% Row Count 20 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{2.33919 cm} x{2.63781 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Matrices}}  \tn
% Row 0
\SetRowColor{LightBackground}
Design or Model matrix \{\{width=27\}\} & Describes the experimental design of the microarray experiment \tn 
% Row Count 3 (+ 3)
% Row 1
\SetRowColor{white}
Contrast matrix & Defines specific comparisons of interest b/w different experimental conditions i.e. defines the hypotheses to be tested \tn 
% Row Count 9 (+ 6)
% Row 2
\SetRowColor{LightBackground}
Types of design matrices & 1. Mean Reference Model (with intercept) \{\{nl\}\} 2. Means model (wihout intercept) \tn 
% Row Count 13 (+ 4)
% Row 3
\SetRowColor{white}
Means model & Mean gene expression levels compared independently for each sample group \tn 
% Row Count 17 (+ 4)
% Row 4
\SetRowColor{LightBackground}
Mean reference model & One sample group set as baseline or reference; gene exp in other groups compared relative to reference \tn 
% Row Count 22 (+ 5)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{X}
\SetRowColor{DarkBackground}
\mymulticolumn{1}{x{5.377cm}}{\bf\textcolor{white}{Design Matrix}}  \tn
\SetRowColor{LightBackground}
\mymulticolumn{1}{p{5.377cm}}{\vspace{1px}\centerline{\includegraphics[width=5.1cm]{/web/www.cheatography.com/public/uploads/lemonbuzz_1694845006_Screenshot from 2023-09-16 11-44-09.png}}} \tn 
\hhline{>{\arrayrulecolor{DarkBackground}}-}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{X}
\SetRowColor{DarkBackground}
\mymulticolumn{1}{x{5.377cm}}{\bf\textcolor{white}{Contrast Matrix}}  \tn
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\mymulticolumn{1}{p{5.377cm}}{\vspace{1px}\centerline{\includegraphics[width=5.1cm]{/web/www.cheatography.com/public/uploads/lemonbuzz_1694845095_Screenshot from 2023-09-16 11-47-38.png}}} \tn 
\hhline{>{\arrayrulecolor{DarkBackground}}-}
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\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{1.89126 cm} x{3.08574 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Microarray Overview}}  \tn
% Row 0
\SetRowColor{LightBackground}
Applications \{\{width=25\}\} & - find expressed genes in a sample/cond \{\{nl\}\} - find diff exp across samples/cond \{\{nl\}\} - exp signatures of sample/cond \{\{nl\}\} - exp signature of set of genes \tn 
% Row Count 7 (+ 7)
% Row 1
\SetRowColor{white}
Limitations & - rely on prev knowledge of genome seq \{\{nl\}\} - high BG levels due to cross-hyb \{\{nl\}\} - complex normalisations needed \{\{nl\}\} - limited range of detection due to BG and saturation signals \tn 
% Row Count 15 (+ 8)
% Row 2
\SetRowColor{LightBackground}
Not good for & - determining exp or diff exp of single or small set of genes \{\{nl\}\} - accurately studying protein levels and functional activity (measure steady-state levels of RNA transcripts) \{\{nl\}\} - absolute level of exp of a gene (true conc of mRNA) \tn 
% Row Count 25 (+ 10)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}


% That's all folks
\end{multicols*}

\end{document}