#### Loading Affymetrix Data (.txt, .TXT) Files

The Expression File Loader (Affymetrix Files)

Selecting Affymetrix Data Files (*.txt) from the drop-down menu allows the loading of Affymetrix files. We currently support five different Affymetrix file format namely: GW Affymetrix, dChip/DFCI_Core, Affymetrix GCOS, Bioconductor (using MAS5) and RMA Files. Select the directory containing files to be loaded using the browse button in the File panel. The contents of the folder selected in the file selection dialog box will be displayed in the box labeled “Available”. Select the files to load and click the “Add/ Add All” button to add them to the list of files to be loaded. Please read Using the Annotation Feature section, for information on the same.

These files contain a single intensity value per spot, instead of the usual two that MeV requires. The values loaded from these files will be used as a Cy5 value, that is, the numerator in the calculation of the ratio of intensities. Therefore there are several options for simulating a second intensity value (the denominator). Select from the radio button options to choose a method. If Absolute is selected, the denominator is given a value of 1 for all ratio calculations. If Mean Intensityis selected, the average of all intensity values for that gene across all loaded Affymetrix files is used as the denominator for that spot. Similarly, if Median Intensity is selected, the median of all intensity values for that spot is used. If Reference is selected, a reference Affymetrix file, selected in the file selector at the bottom of the dialog, is used. The intensity value of each record in the Affymetrix file is used as the denominator of the ratio calculation for the corresponding spot in each of the loaded data files.

#### Automatically Setting Color Scale Limits

When data are loaded in MeV, it automatically generates an expression image. Expression images convey expression levels by converting the numeric expression value (log2 (A/B) or absolute expression value) as a color that is extracted from the color gradient. For Affymetrix data and two channels data, each has different data range in the data set. Now MeV has a new function to automatically sets the color scale limits according to different data sets.

The Expression File Loader (GenePix Files)

For Affymetrix data the low end is set to 0 and midpoint is set as median and high end is set to the value so that 80% of the data fall below this value.

For two color array data the low end is set to -3 and midpoint is set to 0 and high end is set to 3.

Users can change color scale limits after loading as instructed in the following section.

#### Loading Bioconductor(MAS5) Format Files

Bioconductor (MAS5) format file can be loaded by selecting the Bioconductor (MAS5) file loader option from the list of available file formats to load. Use the browse button to locate the files to be loaded. The file will be displayed in a tabular format in the file loader preview table. The call format file generated by Bioconductor can be selected using the browse button in the “Additional Requirements” panel.

Bioconductor (MAS5) Format file loader
Please read Using the Annotation Feature section, for information on the same. Click the cell in the table which contains the upper-leftmost expression value in the file. Click button Load to load file.

#### Loading Affymetrix GCOS Format Files

Affymetrix GCOS (Gene chip operating software) output (pivot data) files can be loaded by selecting the Affymetrix GCOS file loader option from the list of available file formats to load.

This file loader can actually load three similar file formats by choosing data option radio buttons.

> Only Intensity-----only containing signal intensity for every experiment
> Intensity with Detection -----containing detection for every experiment
> Intensity with Detection and p-value-----containing detection and P-value for every experiment

Affymetrix GCOS Format file loader

Use the Browse button to locate the files to be loaded. The file will be displayed in a tabular format in the file loader preview table. Please read Using the Annotation Feature section, for information on the same. Choose the data options by clicking proper radio button. Then click the cell in the table which contains the upper-leftmost expression value in the file. Then click the Load button to load the file.

#### Loading dChip Output Files

dChip File Loader

Selecting dChip/DFCI_core Format Files (*.*) from the drop-down menu allows the loading of dChip or DFCI_core output files. Select the directory containing data files using the Browse button. Files appearing in the Available file list can be added to the Selected file list using the Add or Add All buttons. Please read Using the Annotation Feature section, for information on the same.

These files contain a single intensity value per spot, instead of the usual two that MeV requires. The values loaded from these files will be used as a Cy5 value, that is, the numerator in the calculation of the ratio of intensities. Therefore there are several options for simulating a second intensity value (the denominator). Select from the radio button options to choose a method. If Absolute is selected, the denominator is given a value of 1 for all ratio calculations. If Mean Intensity is selected, the average of all intensity values for that gene across all loaded Affymetrix files is used as the denominator for that spot. If Reference is selected, a reference Affymetrix file, selected in the file selector at the bottom of the dialog, is used. The intensity value of each record in the Affymetrix file is used as the denominator of the ratio calculation for the corresponding spot in each of the loaded data files.