Effect of various normalization methods on Applied Biosystems expression array system data

BMC Bioinformatics

Table 5 Reproducibility of differentially expressed gene lists.

Method	Site1&3	Site2&3	Site1&2	Site1&2&3
Quantile	83.3	81.6	79.8	73.58
Median	83.5	78.1	75.5	70.07
Scale	82.5	78.6	75.4	69.87
VSN	82.4	81.7	78.8	72.49
Loess	83.8	81.2	80.8	74.01
Method	Site1	Site2	Site3	Common
Quantile	619	548	633	507
Median	612	513	634	480
Scale	618	501	612	473
VSN	620	542	619	507
Loess	622	546	628	498

We use t-test controlling FDR at 5% level within each site to detect significantly differentially expressed genes for normalized data. We compare the results for each normalization method, from the 3 sites. First table contains percentage of concordant genes between sites. Second table contains the counts of genes differentially expressed.

ISSN: 1471-2105