Scatterplot of read counts observed in real data for a sample of features.

<p>Scatterplot of raw counts for six representative features displaying counts identified as outliers by <i>iLOO</i> (purple diamond), <i>edgeR-robust</i> (red diamond), and both methods (blue diamond) in the control group of rat RNA-seq data.</p

Flowchart of the iLOO algorithm.

<p>Flowchart of the iLOO algorithm.</p

Venn diagram of the number of features with outliers detected by <i>iLOO</i> and <i>edgeR-robust</i>.

<p>The totals provided present the number of (a) single outlier features and (b) features with two detected outliers identified by <i>iLOO</i> and <i>edgeR-robust</i> in the control group of rat RNA-seq data.</p

Number of features with 0 through 4 detected outliers in the control group of rat RNA-seq data.

<p>Number of features with 0 through 4 detected outliers in the control group of rat RNA-seq data.</p

Comparison of All Transcripts among the Control Groups.

<p>Pearson correlation and scatterplot matrix of log2 normalized expression of all transcripts in control groups, Con1-Con4B. The red solid line is the identity line. Again, the aberrant results of Con4A are due to less than optimal amplification prior to sequencing.</p

Comparison of the Ribosomal Subunit Expression among Control Groups.

<p>Pearson correlation and scatterplot matrix of log2 normalized expression of the ribosomal subunit proteins in control groups, Con1-Con4B. The red solid line is the identity line. Note that the aberrant/anomalous results of Con4A are due to less than optimal amplification prior to sequencing.</p

Citations for Gene Expression within Leukocyte Cell Types.

<p>Citations for Gene Expression within Leukocyte Cell Types.</p

Expression of Selected Immune-Related Transcripts in Control and Amphetamine Treated Rats.

<p>*These genes may also be in dendritic cells as well as monocytes but the levels of dendritic cells are much lower in circulating blood than monocytes.</p><p>**This gene is also present in plasma cells but the levels of these types of cells in blood would be much lower than B cells in circulating blood.</p><p>Expression of Selected Immune-Related Transcripts in Control and Amphetamine Treated Rats.</p

Expression of Ribosomal Subunits in the Control versus Amphetamine Groups.

<p>Pearson correlation and scatterplot matrix of log2 normalized expression of the ribosomal subunit proteins comparing each control group to its time-matched AMPH group. The red solid line is the identity line.</p

Analysis of Leukocyte Cell Types Present in the Whole Blood of Control and Amphetamine Treated Rats.

<p>^a Values for the total and various cell types of leukocytes are measured in thousands (10³) per cubic mm of blood and erythrocyte levels are given in millions (10⁶) per cubic mm of blood. Reported values represent mean ± SEM for blood samples collected from 16 control and 16 AMPH animals.</p><p>^b Reference values for the total and various cell types of leukocytes and RBCs for 56 to 70 day old adult male Charles River Crl:CD(SD) rats were obtained from <a href="http://www.criver.com/files/pdfs/rms/cd/rm_rm_d_cd_rat.aspx" target="_blank">http://www.criver.com/files/pdfs/rms/cd/rm_rm_d_cd_rat.aspx</a>. The mean ± standard deviation levels are given.</p><p>*p < 0.05; Mann-Whitney U test.</p><p>Analysis of Leukocyte Cell Types Present in the Whole Blood of Control and Amphetamine Treated Rats.</p