Fig. 6

Hidden batch attributes. The surrogate variables identified from sva (surrogate variable analysis) are represented in discretized and the original continuous form. These variables are combined with the known variables to generate a prince plot (a) and confounding plot (b). The prince plot (a) reports the association between the first ten principal components of the data and the annotation variables, principal components are represented in the columns, and the sample annotations are represented in the rows. The cell text labels, cell background color, and row label notations with solid blue underline and dotted purple underline are the same as Fig. 4a. The confounding plot (b) reports the association between all pairs of annotation variables; annotation variables are represented in both rows and columns. The cell text labels, cell background color, and row label notations with solid blue underline are the same as Fig. 4a. The row labels underlined with squiggly green line represent known variables associated with surrogate variables. The row labels circled by dotted red outline in (a) and (b) represent the discretized surrogate variables. The row labels circled by solid red outline in (a) and (b) represent the continuous surrogate variables