Gene Expression Data Analysis Suite (GEDAS)

Preprocessing and statistics

Loading Data: Before proceeding further with the experiment, the Experiment name and Experimenter name fields should be filled in promptly.  The next step is to import data. Currently, facility to read tab or space delimited text files as well as to load Microsoft Access and Excel files has been provided in the software.  Whereas the first row specifies sample names, first column indicates the gene names. When a data file is opened for reading, the number of rows and columns is checked and, appropriate error messages gets displayed in accordance with the suitability of data.

A number of options have been provided for adjusting, filtering, removing and computing various statistics of the data loaded. These functions could be accessed via the Filter Data and Adjust Data, Remove Data and Statistics tabs as shown in Figures (a) to (d).

 

(a)

(b)

 

 

(c)

(d)

 Figure Various features of GEDAS (a) The Filter Data tab; (b) The Adjust Data tab; (c) The Remove Data tab; (d) The Statistics tab

Filtering Data: The Filter Data tab can be used to remove genes or samples that do not have certain desired properties from the dataset.  

Adjusting Data: From the Adjust Data tab, a number of very important operations can be performed that alter the underlying data in the imported table. These operations include

·         Merging duplicate data

·         Filling the values of missing data

 ·         Mean/Median Centering

·         Mean Center Genes and/or Arrays

·         Median Center Genes and/or Arrays

·         Normalize Genes and/or Arrays

·         Log transform the data

·         Median center genes and arrays

·         Repeat above step five to ten times

·         Normalize genes and arrays

·         Repeat above step five to ten times

·         Log Transform Data: Replace all data values x by log2 (x).

Removing data: Sometimes, it is very much required to remove unknown genes from the table. This software provides the removing of genes and samples simply by selecting that particular gene or sample. These options are included in the Remove data tab.

Statistics of data: In this software, two statistical tests have been included, viz., the t-statistic and z-statistic.  Following have been implemented in GEDAS:

Sl. No.

Statistic type

Expression

Remarks

1.

Z – Statistic

If  is sufficiently greater than 0 then gene x is unregulated in the population relative to the control

2.

T – Statistic

If  is sufficiently greater than 0 then gene x is unregulated in the population relative to the control

 Table: Statistical techniques implemented in GEDAS

 

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