Raw Data Window

    In cases where there are several attributes identifying a column (e.g. there are two in the below figure), one of them may be used to visually separate groups of columns in the main window.by using the"Select attribute" button. The column of the separating attribute is colored green, as in the below figure, where the columns are separated by stage (i.e., Embryonic, Prenatal, etc.).

Raw Window Attributes

    Table part

• Axis is the number of the column in the dataset. This typically corresponds to one sample on which the expression levels were measured, or one time point in a time series.
• One or more Attribute columns identify a column. This is typically the identification of the sample or of the time point in a time series. For instance, in the above figure the first data column is identified by two attributes: stage "Embryonic" and day "11".
• Clustering
  • Used are the values used by ArrayMiner in computations. This takes into account the possible transformation of the expression values due to the application of log, and/or the selected distance measure (read more on these parameters here).
  • Normalized are the expression values as they were received in the dataset, either from a data file, the clipboard, or by data exchange with GeneSpring. In the last case, the data in this column may be the result of a column aggregation.
  • Raw indicates the expected expression values before normalization using control values.
• ClassMarking
• Used are the values used by ArrayMiner in computations. This takes into account the possible transformation of the expression values due to the application of log, and filter parameters
• Normalized are the expression values as they were received in the dataset, either from a data file, the clipboard, or by data exchange with GeneSpring. In the last case, the data in this column may be the result of a column aggregation.
• For display This column displays the value used for drawing in the classmarker windows. These values are the same as the "Used" values divided by the gene standard deviation. These values are not used to compute classes.
• Control shows the control values used to normalize the raw values in order to obtain the Normalized ones. This column is most useful when the data are obtained from GeneSpring, in that case the values must match the Control values in GeneSpring. When no control values are available in the data, the column contains the value 1 for all columns.

    Graphical part

    The graphical part displays the gene profile. If you select the "Show normalized" checkbox, the profile is drawn using the normalized data values. The normalized profile will be green colored and its maximal and minimal values displayed in the left part of the window. If you select the "Show used" checkbox, the profile is drawn with the used data values. The used profile will be red colored and its maximal and minimal values displayed in the right part of the window. The "Publish" button lets you save the graphical part of the window as a bitmap.