This site provides microarray data analyzed in the following publication:

T. Ideker, V. Thorsson, A. F. Siegel, and L. Hood. Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data Journal of Computational Biology 7 (6) 805-817 (2001).

Several distinct data sets were used. These data are also extremely useful as sample input files to the VERA and SAM software packages. All of these files were generated automatically by the script mergeReps. Click on the numbers to the left of each entry to download:

 Strain/Cond. 1Strain/Cond. 2 Num. GenesNum. RepeatsSection
[1] wt / YPRG wt / YPRG ~6200 (whole yeast genome) 4 Fig. 2a (control)
[2] wt / YPR wt / YPRG ~6200 (whole yeast genome) 4 Fig. 2b and Table 1; text pp. 809-810
[3] wt / YPRG wt / YPRG 96 80 (5 arrays x 16 spots/gene/array) Table 2; text pp. 812


Controlled ratio experiments (Fig. 3)

Labeled GAL80 DNA was spiked into gal80 versus gal80 cDNA at eight controlled ratios of Cy3:Cy5 dye. (Both gal80 strains were grown in YPRG media.) For each controlled ratio, (X,Y) intensity measurements were replicated four times, using microarrays representing 3/4 of the genes in the yeast genome (~4500 genes).

 Controlled Ratiofmol dye / fmol dye
[1] 0.02 0.2 / 10.0
[2] 0.1 1.0 / 10.0
[3] 0.5 5 / 10
[4] 1.0 10.0 / 10.0
[5] 5.0 50 / 10
[6] 10.0 100 / 10
[7] 50.0 500 / 10
[8] 100.0 1000 / 10

NOTE: Due to ongoing improvements to our code, lambda significance values obtained with current versions of VERA and SAM may differ slightly from significance values as reported in the paper.

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