20jun03 - v0.03 1) Updated documentation. 2) Plot key bindings have changed: Double Left-Click: Opens plot option popup window Right Click: Zoom Out 3) Reorganization and reduction of the source code. 4) Small increase in speed of assess expression with technical replicates. 16jun03 - v0.03rc2 1) Added a function to perform the Assess Expression function without Technical Replicates. Technical replication is hybridizing the same labeled mRNA pool to multiple slides. 2) The microsoft binaries are now compiled with Visual Studios .NET. 30nov02 - v0.03rc1 1) Intensity plots and MA Plots have been combined into one tab. Options - right click on the plotted data Zoom Out - Shift and Right click on the plotted data Zoom In - left click and motion to zoom in on a region Broken - Saving the plot will eventually cause a crash The plot is not drag and drop capable 2) Load normalized data. Normalized data files can be reloaded. The only analysis option that can be performed on the normalized data is assess expression. The file must be text tab-delimited and have the following columns (without headers): "channel_1_signal" "channel_2_signal" "geneIDNumber" "normalized_log_ratios" "gene_Number" "gene_Name" See the intensity file description for a definition of the column headers. 10nov02 - v0.03b3 1) cDNA_rank_invariant() has been moved into cDNA_normalization(). 2) mc.c has been converted to mc.cpp; this version will assess the expression of genes even if the calibration is missing for the gene of interest. 3) cDNA_mcsim() McsimDataFile format has changed. New McsimDataFile Format: 1) (***No longer uses a header***) 2) The first two columns are positive floating point numbers. 3) The third column is positive integer; the integers do not need to be unique. 4) The last column is a floating point number; in practice it is the normalized log-ratio of the first two columns. Generally between -1 and 1. 17aug02 - v0.03b2 1) You can load data and a corresponding gene ID file that was created by our "Create Gene ID" function or created with our assistence. We no longer support the geneID file format from prior versions (0.01 and 0.02). 27aug02 - v0.03b2 1) Add [incr Tcl/Tk] support. 2) Add Iwidgets support. 3) Create src/cDNA/tcl_functions/lcDNA_widgets.tcl to house widget creating procedures used in lcDNA. 4) Add scrollbars to the analysis option parameter windows. 5) Switch from lcDNA_help_reader to Iwidget help. 25aug02 - v0.03b1 1) Data can no longer be loaded according to the instructions for v0.02. You must either import data or check "Reload Data" in the "File" menu. The loaded data file format now combines the "gene ID file" with the "data file." The file is a text tab-delimited file (with the .txt extension) do not include a header in your file. There are five columns: 1) Channel 1 = Signal - background intensity for channel 1 2) Channel 2 = Signal - background intensity for channel 2 3) Gene ID # = Integer. Must be the same for the same gene. 4) Gene Number = Sequence / EST identifier 5) Gene Name = current gene name for the sequence. **Again, do not use funny characters (*,&,^,%,$,#,...) or spaces in the file names.