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Table 1 Frequency of preprocessing algorithms used during 2003 – 2008

From: Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity

 

2003

2004

2005

2006

2007

2008

MAS (2002)

8

34

53

42

47

16

RMA (2003)

 

8

15

29

20

9

MBEI (2001)

0

3

7

16

8

3

GCRMA (2004)

  

0

5

8

4

VSN (2002)

0

0

0

4

0

2

  1. Our investigation was performed for 394 different papers with analyses performed using the Affymetrix HG-U133A array (Gene Expression Omnibus (GEO) ID: GPL96) [32]. These results were obtained by reading the entire texts. Statistics for top five algorithms used are shown, and years in parentheses refer to their publication. Suitable methods of ranking genes for the first two algorithms, MAS and RMA, have been discussed [1].
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