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Fig. 1 | BMC Bioinformatics

Fig. 1

From: Practical impacts of genomic data “cleaning” on biological discovery using surrogate variable analysis

Fig. 1

Global transcriptional landscape in differentiating pluripotent cells. PCA of expression data from differentiating pluripotent cells prior to SVA colored by differentiation treatment (a) and microarray scan date (b, left panel). The first PC shows a strong effect of treatment, while the second PC is related to “batch”: boxplots of the second PC indicate strong association with scan date (b, right panel). PCA following estimation and removal of SVs again colored by differentiation treatment (c) and microarray scan date (d, left panel). Both the first and second PC now show systematic association with differentiation, and the second PC no longer shows systematic change with scan date (d, right panel). Letters are also used to distinguish individual scan dates in (b) and (d)

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BMC Bioinformatics

ISSN: 1471-2105

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