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Table 5 Comparison of qRT-PCR with Expresso and TM4. We compare the qRT-PCR results with identified up-expressed and down-expressed genes in Experiment 2 using Expresso and TM4. Results of qRT-PCR are available for each of the four ecotypes in the numbers n in the second column. Numbers of agreement or non-agreement are shown in the S, D, and F columns. The S (same) column tabulates the number of genes for which the sign of the log(fold change) for statistically significant differential expression matches the direction of change in the corresponding qRT-PCR result. The D (differing) column tabulates the number of genes for which the sign of the log(fold change) for statistically significant differential expression is in the opposite direction of the change in the corresponding qRT-PCR result. The F (filtered) column tabulates the number of genes for which there is a qRT-PCR result, but for which either the gene was filtered by MIDAS low intensity filtering or the analysis method did not assess the change in expression as statistically significant. The MEV t-test (first grouping) results are for the typical TM4 process, which involves IIV input data followed by the four MIDAS steps, which we denote IIVTLSF The GP model (second grouping) gives the same numbers and uses the same IIVTLSFinput data, the GP model (third grouping) results use MIV input data and has no filtered genes.

From: The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison

   GP Model GP Model MEV t-test
  qRT-PCR MIV IIVTLSF IIVTLSF
Genotype n S D S D F S D F
Col-0 55 50 5 43 8 4 40 9 4
Cvi-0 52 46 6 38 9 5 36 7 9
ws 59 54 5 46 10 3 41 9 9
Th 26 23 3 21 3 2 19 3 4
Total 192 173 19 148 30 14 138 28 26
Percentage   90.1% 9.9% 77.1% 15.6% 7.3% 71.9% 14.6% 13.5%