Accessing Your Data
This section gives directions for downloading your
data, and gives file descriptions for the Affymetrix® Microarray Suite (MAS) 5.0 data files that are made available
through the Microarray Core. It indicates which files to
use for the available software, and recommends techniques for storing your data.
Downloading your Data
For each sample processed in the lab, five Affymetrix® Microarray
Suite (MAS) 5.0 experiment data files (.CHP, .TXT, .RPT, .EXP, .CEL) will be
returned to the investigator. Each file can be individually downloaded from a
password protected URL which will be communicated to the investigator by the
Microarray Core Director. The data files will be organized by sample in a
figure like the one below. Left click once on the file of interest for the
sample of interest, and follow the directions to specify the location for your
downloaded file. The .TXT, .RPT, and .EXP files are text files that can be
opened directly from the website using NotePad or WordPad. The .CHP and .CEL
files can be opened directly from the website using MAS 5.0.
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Sample Name
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| Chip file (.CHP) |
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| Expression analysis (.TXT) |
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| Report File (.RPT) |
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| Experiment file (.EXP) |
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| Cell file (.CEL) |
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File Descriptions
Click on the icons below for a description of the MAS 5.0 file types available
through the Microarray Core. Much of the information on these pages is taken
from the Affymetrix® Microarray Suite User's Guide, Version 5.0.
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Chip File (.CHP)
The .CHP file contains Signal values and Presence Calls for each probe set on
the microarray and can be viewed using MAS 5.0. The Statistical Algorithm is
used to calculate the Signal values and Presence Calls from the probe-level
fluorescence intensities contained in the .CEL file.
The Signal values and Presence Calls in the .CHP file are organized by probe
set in a pivot table called Pivot. Spreadsheet pages called Analysis Info and
Metrics contain the analysis parameters and metrics used for presence detection
in the Statistical Algorithm. For more information on Signal calculation, see
the Expression Estimates section of
this website. For more information on Presence Calls, see the Presence Calls
section of this website.
Expression Analysis File (.TXT)
The .TXT file is a text version of the .CHP file containing all of the same
information in a tab-delimited format.
Report File (.RPT)
The Report File summarizes background noise, housekeeping information, and
spiked-in controls in the following format for the chip of interest.
Descriptions of the entries in the table are in green. For further information
please refer to the Expression Estimates section of this website, or the MAS
5.0 manual.
example
Experiment Information File (.EXP)
The Experiment Information File is a text file containing sample information,
fluidics settings and scanner settings.
Cell Intensity File (.CEL)
The .CEL file contains fluorescence intensities for each probe on the
microarray. When the .CEL file is opened in either MAS 5.0 or dChip, these
probe-specific intensity values are used to reconstruct the scanned image of
the hybridized array. It is recommended that the investigator view the .CEL
images for each sample to make sure there are no obvious chip defects. For
information on how the values in the .CEL file are calculated from the original
scan, see the Affymetrix® MAS 5.0 Probe-level Analysis section of this
website.
The probe-specific intensities in the .CEL file are also used in the
Statistical Algorithm to calculate the probe-set-level Signals and Presence
Calls recorded in the .CHP file. For information on how the intensity values
in the .CEL file are used to calculate the .CHP file information, see the Presence Calls and Expression Estimates sections of this
website.
Which Files to Use
The files that are necessary to use the software available in the Microarray
Core are listed below.
MAS 5.0
For statistical analysis in MAS 5.0, download the .CHP files into a common
directory and read them into MAS.
To examine the experimental parameters for your samples, download the .EXP and
.RPT files.
To view the probe intensity images, download the .CEL files and read them into
MAS.
dChip
dChip will compute its own Model-Based Expression Indices (MBEIs)
directly from the .CEL files. Download all .CEL files into a common directory.
If the .TXT files are included in the same directory, dChip will use the
presence calls calculated by MAS (this is recommended.)
Cluster/TreeView
Cluster software requires tab-delimited text files of expression values.
The MAS 5.0 .TXT file is tab-delimited, but contains more information than is
necessary for Cluster (i.e. presence calls and presence call p-values). It may
be best to compile the expression values contained in the .CHP files into a
spreadsheet table and save it as a tab-delimited text file.
If you plan to use dChip MBEIs, calculate these in dChip, and then export
the expression estimates as tab-delimited text files.
Please note that TreeView software is used in conjunction with Cluster
software, and that Cluster will export a data set in the appropriate format to
be read into TreeView.
GeneCluster
Two types of data file formats are currently supported by
GeneCluster's file Open... task. One is the WICGR RES file format
(*.res). The other is the GCT (Gene Cluster Text) file format (*.gct). The main
difference between the two file formats is the RES file format contains labels
for each gene's absent (A) versus present (P) calls as generated by
Affymetrix's GeneChip software. GeneCluster also supports loading a CLS file
format (*.cls) for reading in sample class labels. The details of these formats
are described in the GeneCluster reference manual.
If you choose to use expression estimates recorded in the .CHP files, you will
have to do some cutting/pasting/editing to get the files in the correct format.
If you use dChip MBEIs, you can choose the .GCT format when exporting the
expression values.
GeneSpring
GeneSpring can read in tab-delimited text files in a certain format. Neither
the MAS .CHP file nor the expression value output file from dChip are
automatically recognized by GeneSpring. GeneSpring users must first specify a
genome list, and then read in a tab-delimited text file of expression values in
a particular format. For more detailed information on this, please consult the
GeneSpring manual in the Microarray Core Computing Lab or online.
GeneSight
GeneSight has a DataSet Builder that will guide you through the correct format
for your data.
Storing your Data
The Microarray Core is working to develop a database storage system to aid in
the organization of microarray expression data. For the time being, we
recommend storing the necessary files in a common directory on your computer
and/or a disc.
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