Table 1 Quality Assessment Criteria for GPX-MEA

Standard Operating Procedures (SOPs)

Experiment description/protocol

2 – Standard Operating Procedures have been documented and followed.

1 – Only partial SOPs have been documented applied or followed

0 – SOPs not known or not followed

Sample size

Experiment description/protocol

2 – Number of independent biological samples exceeds 5 per group, allowing for reasonably high statistical power in the hypothesis testing.

1- 3–5 independent biological samples per group, allowing to apply minimum level of statistics

0 – 1 or 2 independent biological samples per group (e.g. pilot experiment), reducing the applicability of statistics.

Image quality

Image scan or numerical representation (Affymetrix)

2 – No signs of chip defects, background noise (RawQ) within 5 point range of each other. Scaling factor within 1–2 fold range.

1 – Isolated chip defects, RawQ within 5 point range, scaling factor 1–3

0 – Systematic chip defects, saturation, RawQ outside 5 point range, scaling factor greater than 3.

Target sample quality

Electropherogram, UV-Spectrophotometer

2 – Presence of 18S and 28S ribosomal subunits with no sign of degradation in any sample (RNA integrity). Absorbance ratio of A260/280 close to 2 (RNA purity) [16]. 1 – Either RNA integrity or purity criteria are met. 0 – Neither integrity nor purity criteria are met, or sample quality assessment was not performed, or no information provided.

Sample level data variation/distribution

Box-and-whisker plots, supporting MA plots if required.

2 – Very consistent array medians and Inter-Quartile-Ranges across all samples before normalisation procedures (note: underlying assumption is that any treatments/conditions should not cause differential expression in more than 5–10% of all gene probes on the array.) 1 – Very small number of inconsistent data distributions with assumptions of a correctable difference in array signal intensity met (all genes on array affected, inter-array gene relationships are linear or global differences are expected, e.g. LPS treatment). 0 – Inconsistent median signal levels and spread (IQR) of data throughout the experiment, no biological explanation given.

Gene level data variation

Coefficient of Variation versus Mean Expression plots

2 – Coefficient of Variation for majority of genes across all replicates within a sample group is less than 20%. Genes above this CV level are mostly in the lower signal range (due to measurement error). 1 – A small proportion of all genes has higher CV values than 20%, with a small number of these in the medium to high expression range. 0 – A large proportion of genes has a CV above 20% across most of the expression range.