Determination of variability due to biological and technical variation in urinary extracellular vesicles as a crucial step in biomarker discovery studies

Figures & data

Table 1. Sample size in each group, depending on the effect size (after normalization) and standard deviation, given a power of 80% and α equal to 0.001.

	Effect size (after normalization)
Standard deviation		0.6	0.8	1	1.2	1.4	1.6
	1	98	56	37	26	20	16
	1.2	139	80	52	37	28	22
	1.4	189	107	70	49	37	29
	1.6	246	139	90	63	47	37
	1.8	310	176	113	80	59	46
	2	382	216	139	98	72	56

Table 2. Data on healthy individuals (HIs).

ID	Sex	Age (years)
HI02	Male	55
HI03	Male	57
HI07	Male	53
HI08	Male	69
HI10	Female	59
HI11	Female	52

Figure 1. Experimental set-ups of variation. The total variation is represented by: (a) the instrumental variation (b) the total technical variation (c) the intrabiological variation and (d) the interbiological variation. The names of the samples are indicated.

Figure 2. Number of master proteins per sample in each variation set-up. Samples Pool_1 until Pool_6 were used for the instrumental variation. The samples HI07_pool_1 until HI07_pool_6 were used to calculate the total technical variation. Samples HI07_B/_C/_F/_H/_K/_M were used to determine the intrabiological variation and HI02/HI03/HI07_M (further called HI07)/HI08/HI10/HI11 for the interbiological variation.

Figure 3. Percentage of unique peptides and lipids of the different variation set-ups in the function of the standard deviation (SD) of normalized log intensity. (a) 90% of the least variable peptides of the total variation set-up leads to an SD of 2. (b) The 90% least variable lipids of the total variation set-up do not have an SD that exceeds 1.2.

Figure 4. Boxplot of standard deviation (SD) of normalized log intensity of the different variation set-ups. (a) SD of the instrumental, technical, intrabiological and total variation is shown for the proteomic data. (b) SD of the technical, intrabiological and total variation is shown for the lipidomic data.

Figure 5. Boxplots of coefficients of variance (CVs) of the peptides in the different variation set-ups (instrumental, technical, intrabiological and total variation).