<!-- A simple XML file for the glossary term definitions. Each term is -->
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<!-- the name of the term is supposed to be within a 'word' tag, a short -->
<!-- description within a 'simpleDef' tag and an optional 'completeDef' tag -->
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<glossary>

  <term>
    <word>
      Average dynamic range
    </word>
    <simpleDef>
      The average dynamic range is the mean of the replicate dynamic
      ranges (see replicate dynamic range) for the plate over all the
      replicates.
    </simpleDef>
    <completeDef>
      The average dynamic range is the mean of the replicate dynamic
      ranges (see below) for the plate over all the replicates.
    </completeDef>
  </term>

  <term>
    <word>
      Replicate dynamic range
    </word>
    <simpleDef>
      The replicate dynamic range is an indicator of the gap between
      the positive and the negative controls.
    </simpleDef>
    <completeDef>
      The replicate dynamic range provides an indicator of the gap
      between the positive and the negative
      controls.<br/><br/>Depending on the value of the "scale"
      attribute from the "summarizePlate" function, the replicate
      dynamic range is either: <br/>- the difference between the
      arithmetic average on positive and negative controls <br/>- the
      ratio between the geometric averages on positive and negative
      controls.<br/><br/>By default the choice is based on the scale
      of the data: if the scale is positive, then it is the ratio of
      geometric average, otherwise, it is the difference of arithmetic
      averages.
    </completeDef>
  </term>

  <term>
    <word>
      Repeatability standard deviation
    </word>
    <simpleDef>
      The repeatability standard deviation is the standard deviation
      for the random variable <i>standard deviation for a gene across
	all the replicates</i>. It is used to determine if the results
      for each replicate are similar or not. 0 is the perfect score,
      whereas a high value means the results are very different.
    </simpleDef>
    <completeDef>
      The repeatability standard deviation is the standard deviation
      for the random variable 'standard deviation for a gene across
      all the replicates'. It is used to determine if the results for
      each replicate are similar or not. <br/><br/>0 is the perfect
      score, whereas a high value means the results are very
      different.
    </completeDef>
  </term>

  <term>
    <word>
      Spearman rank correlation
    </word>
    <simpleDef>
      The Spearman rank correlation coefficient is a mesure of
      correlation between two replicates. A result close to zero means
      there is no correlation between the two replicates, whereas a
      result close to 1 means there is a strong correlation between
      them.
    </simpleDef>
    <completeDef>
      The Spearman rank correlation coefficient is a mesure of
      correlation between two replicates. <br/><br/>A result close to
      zero means there is no correlation between the two replicates,
      whereas a result close to 1 means there is a strong correlation
      between them.
    </completeDef>
  </term>

  <term>
    <word>
      Spearman rank correlation (min - max)
    </word>
    <simpleDef>
      This values correspond to the min and the max of the Spearman
      rank correlation among replicates. The Spearman rank correlation
      coefficient is a mesure of correlation between replicates. A
      result close to zero means there is no correlation between the
      two replicates, whereas a result close to 1 means there is a
      strong correlation between them.
    </simpleDef>
    <completeDef>
      This values correspond to the min and the max of the Spearman
      rank correlation among replicates.
    </completeDef>
  </term>

  <term>
    <word>
      Plate List
    </word>
    <simpleDef>
      A table of quality scores for each plate, replicate and
      channel. This also serves as the navigation for drill-down to
      more detailed information for a given set of plates.
    </simpleDef>
  </term>
  
  <term>
    <word>
      Plate Configuration
    </word>
    <simpleDef>
      A graphical representation of the plate configurations. For each
      plate, the physical location of the positive and negative
      controls as well as the position of samples and possibly further
      types of probes are indicated by color coding.
    </simpleDef>
  </term>

  <term>
    <word>
      Plate Summaries
    </word>
    <simpleDef>
      A set of diagnostic plots which provide an overview over the
      general screen quality. In particular, a boxplot of raw and, if
      applicable, normalized data values for the individual plates,
      and dot plots and density plots of the distribution of positive
      and negative controls, but only if the configure function has
      been called before.
    </simpleDef>
  </term>

  <term>
    <word>
      GSEA
    </word>
    <simpleDef>
      A basic gene set enrichment analysis. Output is a table and
      plots of user-defined functions that compute per gene set
      statistics based on the assays scores. Further drill-down is
      available to the actual assays scores of each gene set.
    </simpleDef>
  </term>

  <term>
    <word>
      Screen Summary
    </word>
    <simpleDef>
      A comprehensive plot of the the experiment results. The scored
      values for each plate are indicated by color coding on a
      rectangular grid.
    </simpleDef>
  </term>

  <term>
    <word>
      Screen Results
    </word>
    <simpleDef>
      A table of the experiment result, including annotation
      information and a number of QC values. For data sets of
      reasonable size a condensed sortable table is rendered. Due to
      performance issues there will only be a link to a downloadable
      ASCII file for bigger data sets. The ASCII table contains
      additional information compared to the rendered version.
    </simpleDef>
  </term>

  <term>
    <word>
      Screen Description
    </word>
    <simpleDef>
      Background information about the experiment and about the
      normalization, summarization, and scoring methods that have been
      applied.
    </simpleDef>
  </term>

  <term>
    <word>
      Analysis Script
    </word>
    <simpleDef>
      The R script containing the code instruction to produce this
      report.
    </simpleDef>
  </term>

  <term>
    <word>
      experimentQC
    </word>
    <simpleDef>
      Detailled quality report for a single plate across all
      replicates and channels.
    </simpleDef>
  </term>

  <term>
    <word>
      pdf
    </word>
    <simpleDef>
      Pdf version of the image.
    </simpleDef>
  </term>

  <term>
    <word>
      switchHelp
    </word>
    <simpleDef>
      Switch off the tooltips.
    </simpleDef>
  </term>

  <term>
    <word>
      downloadTable
    </word>
    <simpleDef>
      Download the complete screen result table as a tab-delimited
      ASCII file. You can import this file into any spreadsheet program
      of your choice.
    </simpleDef>
  </term>
  
  <term>
    <word>
      Correlation
    </word>
    <simpleDef>
      The reproducibility of the measurement values between
      replicates. For the case of two replicates, this is a simple
      scatter plot. For more than two replicates we plot the
      correlation matrix. Please note that the assumption of
      correlated data does not hold for all experiment designs; e.g.,
      most of the measurement values could be random noise, in which
      case they would be completely independent.
    </simpleDef>
  </term>

  <term>
    <word>
      Histograms
    </word>
    <simpleDef>
      Histograms of the raw or normalized measurement values for the
      respective replicates. This can be useful to compare data
      distributions between replicates.
    </simpleDef>
  </term>

  <term>
    <word>
      Histogram
    </word>
    <simpleDef>
      Histogram of the raw or normalized measurement values.
    </simpleDef>
  </term>

  <term>
    <word>
      Reproducibility
    </word>
    <simpleDef>
      A plate plot of standard deviations between replicates. Abnormal
      spatial pattern or very high values can indicate problems with
      one of the replicates.
    </simpleDef>
  </term>

  <term>
    <word>
      M-A Plot
    </word>
    <simpleDef>
      Plots of log-intensity averages vs. log-intensity ratios across
      replicates. They highlight the relationship between signal
      variability and signal intensity. If there are more than two
      replicates, a single M-A plot is generated for each one against
      the average replicate values.
    </simpleDef>
  </term>

  <term>
    <word>
      Average
    </word>
    <simpleDef>
      The average (mean) measurement values of a single plate, across
      all replicates.
    </simpleDef>
  </term>


  <term>
    <word>
      Intensities
    </word>
    <simpleDef>
      A plate plot of raw or normalized intensities. Plotting the data
      as arranged on the assay plate helps to identify spatial
      abnormalities.
    </simpleDef>
  </term>

  <term>
    <word>
      Channel Correlation
    </word>
    <simpleDef>
      The correlation of the measurement values between two channels
      in a scatter plot. Depending on the experimental design, the two
      channels can be completely independent, and strong correlation
      could indicate problems.
    </simpleDef>
  </term>

  <term>
    <word>
      downloadStatsTable
    </word>
    <simpleDef>
      Download the result table of the gene set enrichment analysis as
      a tab-delimited ASCII file. You can import this file into any
      spreadsheet program of your choice.
    </simpleDef>
  </term>

  <term>
    <word>
      Scores
    </word>
    <simpleDef>
      Image plot of assay scores, startified by plates. This will be
      clickable if the `map` argument was set to TRUE.
    </simpleDef>
  </term>

  <term>
    <word>
      Q-Q Plot
    </word>
    <simpleDef>
      Normal Q-Q plot of assay scores. Deviations from the line
      indicate non-normally distributed values.
    </simpleDef>
  </term>

  <term>
    <word>
      Distribution
    </word>
    <simpleDef>
      Density plot of the assay score distribution.
    </simpleDef>
  </term>

  <term>
    <word>
      Status
    </word>
    <simpleDef>
      Status of the data import step. In the case of errors, more
      details are provided as a tooltip.
    </simpleDef>
  </term>

  <term>
    <word>
      Filename
    </word>
    <simpleDef>
      Clickable drill-down to the raw data.
    </simpleDef>
  </term>

</glossary>


