Cvt2Mae Frequently Asked Questions (FAQ)

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Q: I was able to convert my data using Cvt2Mae but when I run it with MAExplorer, MAExplorer generates a dry rot error message.

A: This could be a number of things. Most likely it is a parameter that was not set correctly in Cvt2Mae. Double check your parameters. Cvt2Mae does some error checking on parameters and will display the warnings in the status window. Also make sure you data reflects what your parameters are. Sometimes data files can be corrupted ie missing tabs or lines. If you still can not find the problem, email us the dry rot message we will try to help.

Q: I have been using my custom layout to convert data without any problems, but it stopped working.

A: If you had made changes to the original data files such as field names, row and columns, you must also change the corresponding parameters in the Array Layout.

Q: I have a Web database that contains genomic IDs that are not in the normal list and I would like to link my data. Is there a way to set this up in Cvt2Mae?

A: Basically you will have to edit the data files. We recommend using Excel.

Q: Can Cvt2Mae read MAGE-ML XML files?

A: We plan to add the MAGE-ML XML portable array data standard to Cvt2Mae as one of the Array Layouts so it should be able to handle a wider variety of data.

Q: I have a custom chip. How do I convert the data?

A: See the <User-defined> tutorial. This is a screen by screen example on how to convert user defined data.

Q: I would like to merge data from several different projects or adding data from different projects.

A: You can reconvert your data all over again or you can do this by carefully editing the files as described in appendix C of the MAExplorer manual. We recommend merging the data and files from the project directories into a new project directory. You could also merge one set of data into the other, it is better to use the first way. The steps are summarized below.

1. Copy .quant files to same "/Quant" subdirectory

Place all the .quant files into a new "/Quant" subdirectory or one of the existing ones.

2. Edit samplesDB.txt file

The samplesDB.txt files are found in each of the "/Config" subdirectory in the project tree. Details on the parameters are found in appendix C of the MAExplorer manual.
Add all the samples from both files into one file.

3. Create a new Start.mae
The Start.mae files are found in the "/MAE" subdirectory of the project tree. Create a new Start.mae file by merging the two sepatate Start.mae files. The image names must be merged and the X, Y and E lists must also be merged. X, Y, and E lists Correspond to image1, image2, etc.

For example, if you have:

Start.mae file 1 contains:

image1 C57B6-L1-30min
image2 C57B6-L3-1hr

Start.mae file 2 contains:

image1 C57B6-L10-29hrs-1
image2 Stat5a.--.L1-30min

They should be merged to look like:

image1 C57B6-L1-30min
image2 C57B6-L3-1hr
image3 C57B6-L10-29hrs-1
image4 Stat5a.--.L1-30min

4. Example for merging the X, Y and E lists:
X, Y and E lists are optional, but if you want you can merge them also.

The Y, X, E lists are hybridized samples for initial HP-X,Y,E 'set'. They corresponding to image1, image2, etc. Leave them empty if not defined and they may be defined later using the Choose HP-X(Y,E) submenu within File menu in MAExplorer.

File 1

Xlist 1,2,3
Ylist 4
Elist 1,2,3,4

File 2

Xlist 1,2,3,4,5
Ylist 6,7
Elist 1,2,3,4,5,6,7

New Merged file

Xlist 1,2,3,4,5
Ylist 4,6,7
Elist 1,2,3,4,5,6,7

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