Ron Shigeta edited Methods.md  over 10 years ago

Commit id: baa6958b8aa5c2854061f87469b1d20051eb0a70

deletions | additions      

       

Table [1] lists the data sets that were chosen in the Workshop session.   \begin{tabular}{ l c r }   1 & 2 & | Tables | Are | Cool |   | ------------- |:-------------:| -----:|   | col  3 \\   4 & 5 & 6 \\   7 & 8 & 9 \\   \end{tabular} is | right-aligned | $1600 |   | col 2 is | centered | $12 |   | zebra stripes | are neat | $1 |  Overall 10 arrays including replicates of four separate measurements were downloaded as Affymetrix Arabidopsis Genome ATH1 and Rice Genome Array CEL files. These were scaled using the MAS5 algorithm \cite{lim2007comparative} using the 'affy' Biocoductor library \cite{affy2004} in R \cite{R_Core_Team_2013}. The resulting data frame was reduced to mean, median and standard deviation estimates for each probe set for Rice and Arabidopsis each. The results were that the measurement deviation was typically about [get specific %] and the median differed by less that X% from the mean, indicating a reasonable sample variance that was satisfactory where doubling of intensities is considered significant.