Software Standalone applications NucleoDix

NucleoDix

Authors: Roman Jaksik, Joanna Polańska, Robert Herok, Joanna Rzeszowska-Wolny

This program removes multiple probesets corresponding to one gene by removing outlier signals using the Dixons outliers test followed by signal averaging. It searches for gene repeats based on multiple different symbols like Affymetrix ProbesetID, gene symbol or Reference Sequence ID. Program informs about amount of probesets per respective gene, amount of removed outliers and standard deviation between averaged values.

The interface usage can be divided into 3 sections:

1) Data import:

• Import or paste data table with repeated values (columns separated with tabulation sign – like in MS Excel). Imported data will appear in the upper table (nr.4).
• Select column with labels that are going to be analyzed while searching for repeats (key column)
• Select data columns used for calculations from displayed list. (only selected columns are going to be analyzed the rest of them will be ignored)

2) Display options for values shown in the results table

• Show data from key column
• Show amount of probesets removed by the Dixons test
• Show mean value for probe-sets having identical label in key column excluding those, that were removed by the Dixons test
• Show standard deviation between averaged data points

3) Analysis:

• Select input and output symbol type if the key column labels should be translated before looking for repeated values
• You can also chose additional option that will remove only rows (i.e. probesets) that have at least x of outliers in it, individual measures won’t be removed
• Press the “Analyze” button to start the analysis. Results will appear in the lower table (nr.5).
• Save results to a text file (file can be easily opened with MS Excel or text file editors like Notepad)

Available application versions: