Additional file 1 of Assessment of the treating physicians’ first-hand experience with handling and satisfaction of ofatumumab therapy: findings from the PERITIA survey conducted in Europe

Additional file 1. Supplemental material

Mean inter-replicate variance was minimized by applying normalization methods to TLDA cards.

<p> <b>TLDA - Intra-platform.</b></p><p><b>Standard deviation</b> Legend information as specified for <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038946#pone-0038946-t001" target="_blank">Table 1</a>.</p

Impact of normalization strategies on the similarity of differential miRNA expression of AGL array data.

<p><b>Agilent - Intra-platform Jaccard index</b> The mean Jaccard indices of significantly regulated miRNA overlap across normalized datasets were depicted for myoblast differentiation and cytokine treated samples analyzed of human and mouse. The Jaccard index ranges between zero and one per definition. The closer the Jaccard index is to one the higher the relative similarity and reproducibility of differential expression across platforms.</p

Platforms and normalization methods applied.

<p>Overview of intra- and inter-platform comparisons using miRNA microarrays from Agilent Technologies (AGL Array) and RT-qPCR arrays from Applied Biosystems (TLDA) for human and mouse miRNAs as well as singleplex TaqMan miRNA assays. Different normalization methods were applied to the platforms. Three distinct biological stages of mouse and primary human skeletal cells were analyzed.</p

Effect of normalization methods on the number of differentially expressed miRNAs detected by TLDA cards.

<p> <b>TLDA - Intra-platform.</b></p><p><b>Significant miRNAs</b> Legend information as specified for <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038946#pone-0038946-t005" target="_blank">Table 5</a>.</p

Signal distribution of human microarray and qPCR profiling.

<p>Box-whisker plot with 5th and 95th percentiles (black dots) of log2-transformed human AGL array signals or Cq values of human TLDA platform were shown for nine samples each across different normalization techniques.</p

Mean area under the ROC curve of the inter-platform miRNA subsets for TLDA cards.

<p> <b>TLDA - Inter-platform.</b></p><p><b>ROC curves</b> Legend information as stated for <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038946#pone-0038946-t009" target="_blank">Table 9</a>.</p

Mean inter-replicate variance was minimized by applying normalization methods to the AGL array.

<p> <b>Agilent - Intra-platform.</b></p><p> <b>Standard deviation.</b></p><p>The average of intra-replicate standard deviations in human and mouse myoblasts, myotubes, and cytokine treated myotubes based on the platform-specific miRNA datasets were depicted. The mean intra-platform standard deviations depended on the normalization method.</p

Impact of normalization strategies on the similarity of differential miRNA expression of TLDA card data.

<p><b>TLDA - Intra-platform Jaccard index</b> Legend information as stated for <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038946#pone-0038946-t007" target="_blank">Table 7</a>.</p

Effect of normalization methods on the number of differentially expressed miRNAs detected by AGL arrays.

<p> <b>Agilent - Intra-platform.</b></p><p><b>Significant miRNAs</b> The mean number of differentially expressed miRNAs which were identified in distinctively normalized human and mouse myoblast differentiation and cytokine treated samples were depicted.</p