File Loader
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File Formats
MeV supports the loading of several file formats. For a complete
description refer to the manual included in the documentation
folder appendix 11. Here's a brief overview of supported file types.
mev Format (Multiple Experiment Viewer Format)
This format is a tab delimited text file format which allows a header
for identification of columns and comments are preceded by the pound (#) sign.
The first nine columns are a unique identifier, slide row, slide column,
meta row, meta column, sub row, sub column, intensity 1, intensity 2. The unique
identifier is used to match up corresponding annotation which is supplied from
annotation files which contain spot annotation for each element on the slide.
The annotation files, given a .ann extension are also tab delimited and
have entries corresponding to the unique identifiers in the mev file.
One or more annotation files may be loaded to provide several types of
annotation.
Tab Delimited, Multiple Sample (TDMS) Format
The TDMS format file encapsulates several hybridizations in one file.
The first several columns are used for annotation and following the
annotation the intensity data corresponds to one column of log2ratio(cy5/cy3)
for each hybridization. The format includes a header to identify the
labels for the annotation as well as the labels for the individual hybridizations.
tav Format (TIGR Array Viewer Format)
This is similar to the mev format but differs in that it does not permit
a header row or comment rows and there is no unique ID column. Each tav file contains
annotation following the columns for intensity and other spot specific information.
The loading of tav files depends on having selected a 'preference' file which is used
to identify the type and number of annotation fields in the tav files.
Affymetrix File Format
Affymetrix arrays use a single dye system. The file description is detailed on
the Affymetrix web site but includes a Affy probe identifier, an intensity
value, a detection flag to indicate whether or not a spot signal is present or absent,
and a spot description.
Gene Pix File Format
Loading Files
Loading requires several basic steps that vary slightly depending on the file
format chosen.
1.) Select a file format.
2.) Select a directory using the file navigation tree in the left window
until the selected files are reached.
3.) Select the data file or files.
mev Format
For mev format you will select several data files in the available files list
and use the add button to move them into the selected file list box. The same
process is used to select one or more annotation files. Once these files are selected
hit the OK button to load the files.
Tab Delimited, Multiple Sample (TDMS) Format
For TDMS format you will select a path to the data file and once a file
is selected a table will display the first few rows of the file. Select the
first log ratio of the first, left most, hybridization in the table. This will
identify the upper left limit of the log ratio data. Columns to the left contain
annotation while columns above contain header information. Once the proper cell
has been selected the annotation field names should appear in a window near the bottom
of the form. Select OK to load.
tav Format
For tav Format there are several means to load the files. The most common is to
use a preference file to indicate annotation fields in the file. See the manual
for a full description of the tav format and the use of preference files.
Navigate through the tree to select the tav files then use the file browser button
to select an associated preference file.
Affymetrix Format
There are four modes to loading Affymetrix files.
1.) The absolute selection simply loads
the single intensity value into one channel and sets the other channel to 1.0.
This will require the user to scale the expression image, set ratio scale, to
increase the dynamic range of the image to compensate for the absolute intensities.
2.) The mean and median modes are related. For each spot the intensity is averaged
or the median is taken across the hybridizations (files). This average value is used as a reference to
scale the intensities corresponding the that spot. Each spot gets assigned one intensity
to the spots true intensity and the other intensity is set to the mean or median
intensity. The calculated log2(r) is taken where
r = (spot intensity)/(ave. intensity)
3.) The reference loading mode allows the user to select a file to represent
a reference against which the other files are compared.
log2(spot intensity/ref. intensity)
Please refer to the manual for more details and information regarding file formats
and loading data.