Factors and batches (N) by which fathead minnow (PPR) and zebrafish (DRE) microarray samples were organized.

<p>Sample sizes were indicated in parenthesis.</p><p>BPA, bisphenol-A; EE2, 17a-ethynyl estradiol; FAD, fadrozole; FIP, fipronil; FLU, flutamide; GEM, Gemfibrozil; KTC, ketoconazole; PRO, prochloraz; RDX, hexahydro-1,3,5-trinitro-1,3,5-triazine; TRB, 17 -trenbolone; TNT, 2,4,6-trinitrotoluene; TRI, trilostane; VIN, vinclozolin; WLSSD, effluent from Western Lake Superior Sanitary District; RNA Date not determined: 11111, 55555; RNA Person not determined: DDD, YYY.</p><p>Factors and batches (N) by which fathead minnow (PPR) and zebrafish (DRE) microarray samples were organized.</p

Within-batch variation as measured by coefficient of variation (CV).

<p>The CVs were calculated for each probe by individual batches under the Experiment factor and averaged over all batches. Further averaging these CVs across the entire transcriptome yielded an overall CV of 0.056 for fathead minnow (PPR) and 0.051 for zebrafish (DRE). The total number of orthologous genes identified between Agilent 015064 and 019597 was 6617, represented by 9311 and 6950 unique probes respectively. The PPR probes mapped to their EST sequences and ESTs to NCBI databases by BLAST all had a minimum E-value of E-06.</p><p>Within-batch variation as measured by coefficient of variation (CV).</p

Interspecific correlation by average intensity and average coefficient of variation of individual pathways.

<p>A total of 84 (three outliers excluded) KEGG pathways were calculated for their average intensities (A), and 53 (two outliers excluded) pathways for their average CVs (B), based on a combined total of 6617 orthologous genes. To be included, each pathway must have at least five orthologs and a p-value of ≤0.1 for the correlation of the intensities or CVs of its member genes as estimated within a batch. The CCs were 0.86 and 0.80 for the average intensity and average CV by pathway respectively, with the both p-values = 0. The p-values of normality test of error distribution for linear regressions were 0.045 and 0.585 respectively.</p

Interspecific correlation by within-batch intensity and coefficient of variation of orthologs.

<p>The within-batch intensities (A) and coefficients of variation (CV; B) were based on 6617 orthologous genes. The orthologs were represented by 9311 zebrafish (DRE) and 6950 fathead minnow (PPR) probes. The intensity and CV of an ortholog with duplicated probes were probe means. The correlation coefficients over the orthologs for the two metrics were 0.49 and 0.33 respectively, with the both p-values = 0.</p

Within-batch variation as measured by the maximum (% of transcriptome) and minimum number of DEGs per permutation.

<p>There were 250 permutations conducted under individual factors. Between-batch variation was controlled statistically in these analyses. PPR, fathead minnow; DRE, zebrafish.</p><p>Within-batch variation as measured by the maximum (% of transcriptome) and minimum number of DEGs per permutation.</p

Intraspecific correlation between the average CV and average intensity by KEGG pathways.

<p>A total of 136 pathways (eight outliers excluded) were included for fathead minnow (A) and 144 pathways for zebrafish (B). The CCs were −0.68 and −0.70 respectively, with both p-values = 0. The p-values of normality test of error distribution for linear regressions were 0.094 (no significant departure from normality) and 0 (significant non-normality) respectively.</p

Between-batch variation as measured by average number of DEGs (standard deviations where N>3).

<p>The DEGs were identified in paired comparisons of N–1 batches against a batch designated as a common reference. N is the total number of batches in a factor. The comparisons were made in conjunction with the analysis of within-batch effects involving 250 permutations. There were little variations in between-batch effects among permutations so their calculations were made only from the first permutation. DRE, zebrafish; PPR, fathead minnow.</p><p>Between-batch variation as measured by average number of DEGs (standard deviations where N>3).</p

Percent agreement between experts on final pass/fail result of papers tested in Round 3.

<p>Each paper was tested through the SOAR tool by 3–5 expert experts. Paper 13 had no agreement between the three experts due to misunderstanding of the data presented in the paper. Paper 17 had 1 of 3 experts disagree.</p

Question sections included in the original version of the SOAR tool compared to the final version.

<p>The section "Test System" has different questions based on the type of study. The maximum number of questions a paper can require is 34, though only 29 of them would be scored. The first five basic questions are used to exclude inappropriate papers and to set up the questions required, and are therefore not given a score.</p><p>Question sections included in the original version of the SOAR tool compared to the final version.</p

Results from Round 4 of testing.

<p>Though some authors disagreed on specific answers to certain questions, the disagreement was not significant enough to change the final outcome for the papers. Paper 9 and 10 passed; paper 11 and 12 failed. For paper 12, EM, SB, LB, and NGR failed the paper in the “Basic Questions” section based on a lack of sufficiently biological replicates (tool requires n≥3), and therefore the following question sections were not answered. RW and PG did complete all the question sections, however, the paper still failed.</p><p>Results from Round 4 of testing.</p