Open Access Research article

Batch correction of microarray data substantially improves the identification of genes differentially expressed in Rheumatoid Arthritis and Osteoarthritis

Peter Kupfer1, Reinhard Guthke1, Dirk Pohlers23, Rene Huber24, Dirk Koczan5 and Raimund W Kinne2*

Author Affiliations

1 Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany

2 Experimental Rheumatology Unit, Department of Orthopedics, University Hospital Jena, Friedrich Schiller University, Jena

3 Present address: Center of diagnostics GmbH, Chemnitz Hospital, Chemnitz, Germany

4 Present address: Institute of Clinical Chemistry, Hannover Medical School, Hannover, Germany

5 Institute of Immunology, University of Rostock, Rostock, Germany

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BMC Medical Genomics 2012, 5:23  doi:10.1186/1755-8794-5-23

Published: 8 June 2012

Additional files

Additional file 1:

Table S1. Mean expression values of differentially expressed genes of interest in RA and OA patients with and without BC for all time points.

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Additional file 2:

Figure S1. Hierarchical clustering of uncorrected and batch-corrected data from time point 0: a) The uncorrected data form clusters reflecting the 2 different years of acquiry (red shades for arrays generated in 2006; blue shades for those generated in 2009). In contrast, RA and OA are not grouped. b) The ComBat-corrected data (2 batches) still fail to form clusters reflecting the diseases (RA and OA).

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Additional file 3:

Figure S2. Cluster plots for the time points 1, 2, 4, and 12. a) Time point 1: TNF-α. b) Time point 1: TGF-β1. c) Time point 2: TNF-α. d) Time point 2: TGF-β1. e) Time point 4: TNF-α. f) Time point 4: TGF-β1. g) Time point 12: TNF-α. h) Time point 12: TGF-β1.

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Additional file 4:

Figure S3. Means and variances of differentially expressed genes from the uncorrected data set (DEG_woBC) in RA (a) and OA (b) patients with (red dots) or without BC (blue dots); there are generally only marginal changes of the means, but moderate to substantial reductions of the variances.

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Additional file 5:

Table S2. Comparison of the power values for the differentiation of RA and OA before and after BC for the differentially expressed genes [applied values: means ± standard deviations (SD)] calculated using GPower [25].

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Additional file 6:

Table S3. Differentially expressed genes calculated with LIMMA for 20 permutations.

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Additional file 7:

Figure S4. Cluster plots for time point 0 on the basis of 20 permutations of the disease status (RA and OA).

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Additional file 8:

Table S4. Mann–Whitney U tests for the comparison between RA and OA in a), or for the comparison between TNF-α and TGF-β1 in b); +, significant difference; -, lack of significant difference; *, significance test is not applicable (technical replicates).

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