Single self experiments have been categorised as self indulgence or abuse, and trivial interventions masquerading as research studies as a source of amusement.
To check whether culture condition (with the heavy isotope) could influence the protein quantification, we performed a self-self experiment with LAU-Me275.
The theoretical outcome of any self-to-self experiment is clear: absolute expression values for genes should be identical across array dye-label channels.
In the same interval, we identified 1 up-regulated and 2 down-regulated genes for the self-to-self experiment, giving an estimated overall FDR of 3.26%.
In contrast, a much broader distribution was observed for the gene specific probes in the differential gene expression experiment, with distribution of the control oligos similar to that in the self-to-self experiment.
Although our microarray is based on strain NCTC 11168 the resulting LRs should remain close to zero because, regardless of the strain used in the self-self experiment, "Control" and "Tester" targets are identical.
Differential gene expression between CD26+ G3 cancer cells and CD26+ luminal cells analyzed by HTself identified 121 genes with increased cancer expression and 86 genes with decreased cancer expression by at least 8-fold relative to luminal cells (see Additional File 1 for full list, and Additional File 2 for self-self experiment and HTself cutoff for differential expression).
As we did not perform a self-to-self experiment, a stringent criterion with the mean |log2 ratio| > 0.5 was used to reduce the false positive rate of CNV calling according to the studies of Wang et al. [ 19] and Fadista et al. [ 28].
For all 12 of the wine yeast isolates, we observed hybridization patterns much more similar to that of the "self-self" experiment, i.e., with robust signals across most of the array, and the majority of ratios near a value of 1.0.
Since the FPR can be overestimated from sex-mismatched arrays, due to the assumption that no CNV exist in the chrX of sex-mismatched arrays, the FPR was also calculated from the self-self experiment and was determined as the length of sequence that would normally be called a CNV with our CNV calling pipeline.
To find genes at a specific false discovery rate (e.g. 0.05), T-scores computed for the high contrast and the self-self experiment are sorted and the T-score cut-off is lowered until the chosen false discovery rate is obtained.
