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. 2010 Mar 26;5(3):e9905. doi: 10.1371/journal.pone.0009905

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This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.

This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.

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The SWISS scores for the reference design (solid red) and single channel design (dashed blue) along with corresponding 90% confidence intervals (black bars) calculated from the SWISS permutation test are shown for dataset I. The genes for both designs in A were filtered according to variance across all arrays in the single channel design, and the genes in B were filtered according to variance across all arrays in the reference design. The SWISS scores in B are lower than those in A, which suggests that filtering genes using the reference design is better than filtering genes using the single channel design. Also, there are gene filterings in both A and B where there is no significant difference between the single channel and reference designs (both the red and blue lines lie inside the black bars).