Biology Reference
In-Depth Information
EXPANDED DISCUSSION OF ZERO COUNT STATISTICS
This section contains an expanded discussion of the analysis of signa-
tures that yield zero counts in one or more (but not all) of the MPSS
sequencing runs constituting a given signature library. In this analysis,
only basal measurements are considered (unperturbed macrophages,
i.e.,
t
0 measurements), and of these measurements consideration is
further restricted to TS measurements. Exemplary measurements are
shown in table 4.1. In this table, B1:1 indicates MPSS run 1 for biolog-
ical replicate 1 of macrophages in their basal state (B stands for basal),
and B1:2 indicates MPSS run 2 for the same sample. Likewise, B2:1 and
B2:2 indicate the same for the second biological replicate. One con-
spicuous feature of the data is the appearance of many signatures for
which there is one zero in one of the MPSS runs (e.g., B1:1, signature 2
in table 4.1) and a nonzero in the companion MPSS run (B1:2).
Continuity arguments may suggest that if the count of a signature is
zero in one run, then it should be small in the other. However, one
can readily see that there are signatures that were not measured in
three MPSS runs, but were measured in 476 beads in one of the runs
(B1:2, signature 6). Likewise, continuity suggests that the statistical
behavior observed for sequences for which a zero count is measured
in one of the runs must be similar enough to the statistical behavior of
the signatures observed at low but positive counts such as 1, 2, and so
on. Figures 4.10a and 4.10b (for which the axes are in bead counts,
rather than in tpm) show that for comparisons between B1:1 and B1:2,
and for comparisons between B2:1 and B2:2, respectively, the behavior
at zero is quite different from the behavior at 1 (in the log-log plot,
the log of 0 was replaced by the log of 0.5 for clarity). For example, there
=
Table 4.1 Exemplary signatures and measurements for basal macrophage
gene expression
B1:1 B1:2 B2:1 B2:2 Nomenclature
Signature 1 8 17 15 25 Nonzeros in B1, nonzeros in B2
Signature 2 0 4 5 11 One zero in B1, nonzeros in B2
Signature 3 3 8 2 0 Nonzeros in B1, one zero in B2
Signature 4 22 42 0 0 Nonzeros in B1, two zeros in B2
Signature 5 0 0 15 7 Two zeros in B1, nonzeros in B2
Signature 6 0 476 0 0 One zero in B1, two zeros in B2
Signature 7 0 0 625 0 Two Zeros in B1, one zero in B2
Signature 8 0 23 0 115 One zero in B1, one zero in B2
Signature 9 0 0 0 0 Two zeros in B1, two zeros in B2
The signatures show different possible combinations of zero and nonzero measurements
(B1:1, B1:2, B2:1, and B2:2) for two MPSS replicate measurements taken for each of two
biological replicates (B1 and B2).
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