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To have For a
fair fairer comparison to Foll et
all al \citep{Foll2014}, we
put aside the last time point sample and apply applied our method to the joint data
of from Passages 1, 3, 9, 12
with for both the control and treatment groups, i.e. $t_1, t_2, t_3, t_4, t_{3D}, t_{4D}$. The summary statistics used are
\begin{equation}
...
& 2 & 10.435& 80 & 729, 819\\
\hline\\
\end{tabular}
\caption{Result derived using \caption{Our approach identifies only one true signal when data from only Passages 1, 3, 9, and
12. 12 are used. The thresholds and corresponding signal \& noise sets for each segment according to each biological replicate. The sites identified as signal in both experiments are highlighted in red, the ones identified as noise in both experiments are highlighted in blue. Fewer substitution sites
are were identified
comparing compared to previous table (see Table \ref{tab:H1N15t}).}
\label{tab:H1N14t}
\end{table}
Taking the intersection of the findings from both replicates, we identify only S6-822 as a substitution site due to the
treatment, along with treatment. Several other sites, S1-2299, S2-2303, S3-173, S3-174, S3-176, S3-176, S3-200, S3-203, S3-2078, S3-2192, S3-2193, S3-2195, S5-24, S5-389, S5-1103,
S6-977 S6-977, were identified as
the locations with large variation not due to the treatment.
Comparing the result Intriguingly, most sites identified in Foll et al \citep{Foll2014}
to our findings (Table
\ref{tab:H1N14t}), we notice that all the extra locations identified there \ref{tab:H1N14t}) appear in
the result for our analysis to only have signal in the first biological
replicate, but not replicate. The exception, S6-822, has a strong signal in
both replicates and regardless of end point generation analyzed (figure ...). We speculate that the
result for lack of consistent signal/false signal coming from the
second. This phenomena other sites is
likely caused by the
fact that the lower average read count per site for the second replicate
is much smaller than compare to the first. The
analysis in Foll \citep{Foll2014} based on a population genetic approach
therefore used in Foll \citep{Foll2014} appears to be heavily influenced by the first replicate. This leads us to postulate that their result is adversely affected by the large imbalance in counts.
Noticing that the two additional sites identified in Table \ref{tab:H1N15t} show more pronounced drug effect after the 12th passage (see Figures \ref{fig:S5-300},\ref{fig:S8-80}). We conclude that IVA had not fully responded to the treatment by Passage 12 and our previous analysis, including the last time point collection, is more reliable for the identification of substitution sites.
