Microbial Diagnostic Array Workstation (MDAW) is a Web server for diagnostic array data storage, sharing and analysis. Since it’s online, its not platform dependent and with an internet connection you can access and analyze diagnostic array data from anywhere. And this is a completely free resource.
Back to topIf you like to know more about various types of diagnostic arrays and data analysis methods used, See this page for a list of recent reviews and This page for list of recent articles on diagnostic arrays.
Back to topPlease click here to download a quick start guide on how to do Ad-hoc analysis in MDAW. The analysis options in both registered user mode and ad-hoc analysis mode are same. So you can use this quick start guide for both modes.
Back to topMDAW has two modes of use. The first mode is registered user mode and the second is Ad-hoc analysis mode. In the registered user mode, you will need to complete registration step for access and Ad-hoc analysis does not require registration and is quick way to access MDAW analysis pipeline.
Back to topThe registered user mode allows you to access the full functionalities of MDAW. To access this, you need to complete the registration step. The information submitted for registration is not shared and your data is never shared. Upon registration, you will be given 1GB of space in the server. You can use this either for storing your raw data files or for storing the analysis results. This mode also allows you to add additional users to your project for file and result sharing. You can designate yourself as the project administrator/principal investigator and specify other users access rights. If you do not add any other user, only you will have access to your files.
Back to topAd-hoc analysis is an easy mode of access to MDAW. This does not require any registration. All the analysis options available to the registered user are also available in this mode. The difference between this and the registered user mode is that in Ad-hoc analysis mode you will not be able to store any data or results in the MDAW server and you will need to store all results to your local computer for future use.
The file format permitted in MDAW are Genepix pro format (.Gpr) and Tab delimited text (.txt). Of these two formats, the .Gpr format is set as default. If you are not familiar with the details of .Gpr format, see this page at Molecular Devices for details. Here is some sample .Gpr files.
If your data is any other formats, you can convert your data into a tab delimited file and then upload to MDAW. For doing this, open your data file in a spreadsheet programme like Microsoft Excel and then choose the option file, save as and then from pull down menu select Tab delimited text as the format.
You can upload any number of permitted file types until you reach the limit of 1GB storage space allowed for you. After you login, go to File---> Upload and then click on browse button and locate your files on your computer and click upload button to upload.
While uploading, you also need to assign the following attributes to each file using the file upload menu
Project name:
Choose a project name from the pull down menu. If you have not yet added any project names, go to projects on the left side menu and then add a project name. Before you can upload a file, at least one project name should be specified.
Experiment name: You can add one experiment name for a file. This helps you organize your files with in a project. One project can have files with different experiment names.
Date: Add a date to the file. It can be any date (means it could be a date other than the date of uploading the file). This will again help your to organize the files; for example in the chronological order of dates on which you performed your experiments or based on the dates which you uploaded your files.
Tags: Add at least one tag for each file. You can have one or more tags for a file. This will help you to search for the files using the list of tags which you specify.
Before the uploaded files could be analyzed, the column headers of the uploaded file need to be mapped. Mapping is a process in which you equate the required column headers with the corresponding column headers in the uploaded files. The requires columns in MDAW are
Probe name
Signal median
Signal mean
Background Median
Background Mean
SNR (Signal to noise ratio)
Flags
A GPR file which was generated from a Cy3 (green wavelength, 532nm) labeled hybridization, can be mapped as
Name = probe name
F532 Median = Median probe signal intensity
F532 mean = Mean probe signal intensity
B532 Median = Median background signal intensity
B532 Mean = Mean background signal intensity
SNR 532 = Signal to noise ratio
Flags
A GPR file which was generated from a Cy5 (red wavelength , 635nm) labeled hybridization, can be mapped as
Name = probe name
F635 Median = Median probe signal intensity
F635 mean = Mean probe signal intensity
B635 Median = Median background signal intensity
B635 Mean = Mean background signal intensity
SNR 635 = Signal to noise ratio
Flags
For example, below are the steps for mapping the probe name (required column) with name column in GPR file.
1. Click on the column name that is required
2. Click on the corresponding column name from the uploaded file
3. Click on the map button. This will show the mapping result in the mapped columns area.
See the picture below for example.
Repeat these steps for all required columns.
If your data is in a tab delimited file format, MDAW still reads it. For mapping the headers for such files, do the same steps mentioned above and equate the column headers in your file to the required columns.
Files menu provide options for managing files in MDAW. You can track and search files based on Project name, experiment name, date and tags. Principal investigators have full control on file access rights. If you are ordinary users in a project, your access rights will be set by the Principal Investigator of the project.
All registered users can download any raw data files from the file management page. MDAW does not modify your data files. All the results files also can be downloaded as the tab delimited text (.txt). After saving these tab delimited files to your computer use Microsoft Excel or similar programme to view them.
The analysis options page shows the selected files in the first row. There are five steps you need to do before calculating the summary statistics of the probes.
A. Select column to analyze: need to select type of signal in your file for analysis. Any one of the three signals shown below can be selected from the pull down menu.
Mean signal Intensity
Median signal intensity
Signal to noise ratio (SNR)
B. Background correction. The following options are available and you can select any one.
(i) Half
This method is designed to produce positive corrected intensities. Any intensity which is less than 0.5 after background subtraction is reset to be equal to 0.5.
(ii) Minimum
This method is designed to produce positive corrected intensities. Any intensity which is zero or negative after background subtraction is set equal to half the minimum of the positive corrected intensities for that array.
(iii) None
The corrected intensities are equal to the foreground intensities, i.e., the background intensities are treated as zero.
(iv) Subtract
This function simply subtracts the background intensities from the foreground intensities which is the usual background correction method.
C. Set missing values: (this is not available if SNR column is used for analysis )
Constant value ( user need to enter a value)
Fill with signal mean
D. Log transformation. If you select this option, the signal values are converted to the equivalent log2 values. We strongly suggest selecting this option.
E. Select an annotation file. This is an optional step. If you upload an annotation file, the results will be combined with the annotation provided. Annotation file also can be used for calculating results for a subset of probes or for arranging the results in a particular order. See the next section for more details on how to use annotation file.
Using annotation file in the analysis is an optional step. If you are uploading an annotation file, it has to be in comma separated value (CSV) format.
Click here for a sample annotation file. Normal excel and tab delimited files will not work. You can create such a CSV file by typing the details in Microsoft Excel and then saving it as comma separated value file. The column header names should not have any spaces in them and should have the following mandatory columns.
Sortorder: This column is mandatory and should have the order in which you want the probes to be arranged in the results. Probes in the arrays are usually printed/synthesized in random order. You can use this option to arrange the results in the way you want.
Probename: This column is mandatory. The name of the probes in the array. This has to exactly same as that of whatever name your probes have in the array.
Genename: The name of the gene for which the corresponding probe is designed. If you do not have this information, you can leave this blank, but you need to have this column with a valid column header named as “Genename”.
Sequence: The sequence of the probe. If you do not have this information, you can leave this blank, but you need to have this column with a valid column header named as “Sequence”.
If you don’t have the information for each of these columns, still make a column with that name and then leave it as an empty column.
An annotation file can be used for various purposes in MDAW.
A. Arranging the probes in a particular order in the results. Probes in the microarrays are synthesized/printed in a random manner. However by proving the annotation file with the sortorder, the results will be arranged in the order given in sortorder column.
B. Analyzing the values of only a subset of probes in the array. If you provide an annotation file with a subset of probes in the array, then results will be calculated only for the probes given in the annotation file. You ca use this option to calculate the summary statistics of the housekeeping/common genes in your array.
C. Combining the annotation and with the results. By providing the annotation file, you can combine the annotation with the calculated results. This will help you understand the results of each probes in the context of corresponding annotation.
Calculating the summary statistics help you decide the final cutoff. By default the summary statistics is displayed, but you can download it by clinking on the download button in the summary statistics results page.
