Table 1.
Prevalence and impact of technical factors that constitute potential sources of batch effects in gene expression experiments. The second column shows the percentage of samples that are critically affected by the respective technical artifact. The selection of appropriate thresholds is reasoned in the respective subsections. Column two denotes the prevalence among all samples in the HumanArraySet, in column three among the subset of samples that have been selected after quality control independently performed by [7]. Column four shows the correlation of the technical variable with the principal components of the expression space, and last column how it changes along with known batches.
| Parameter | Prevalence (all) | Prevalence (qc Included) | Correlation with Principal Component (pc) | Adjusted R2 with Batch (Lm) |
|---|---|---|---|---|
| Degradation index dk | 10.6% | 3.0% | −0.44 (2) | 0.67 |
| Specific transcript level λ | 1.6% | (0.1%) | −0.61 (4) | 0.62 |
| Measuring range β | 4.2% | (0.1%) | 0.04 (1) | 0.24 |
| Sequence effect size | 4.1% | (0.1%) | −0.17 (3) | 0.76 |
| Guanine effects | 3.1% | 1.1% | 0.19 (5) | 0.76 |