affy Transcriptome Analysis Console (TAC), export expression matrix?
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18 months ago
RNAseqer ▴ 180

Hello everyone,

I am starting to work with the Affy Transcription Analysis Console (TAC) on some miRNA4.0 data. I would like to output an expression matrix after RMA normalization/summarization. of the miRNA data. I see from the old Affymetrix Expression Console that there was a way to do this:

https://ambystoma.uky.edu/genome-resources/10-webpages/24-instructions-for-performing-rma-analyses-in-expression-console

however, the Affymetrix Expression Console has been discontinued, its functions are now included in the TAC software. However, I cannot seem to find instructions in the TAC manual for how to accomplish this process. I know that many of the downstream analysis tools are included in the TAC software but I NEED to extract this expression matrix for use elsewhere.

Has anyone had success in doing this? Thanks!

affy TAC expression matrix • 715 views
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As this is commercial software, use their Support service.

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Just got off the phone with the affy people. Here is how you do this for TAC 4.01:

You must do an analysis even if you dont intend to use its output in order to get to the menu option that allows you to export your expression table. So, load in your .cel files using "import cel files in the upper left corner of the first screen, you should also have downloaded the appropriate library from the affy site. I stored mine in the same folder as my .cel files.

having loaded some cell files, there should now be a 2 columns one "File Name" with your cel files, and the next "Condition" I selected my type as comparison and of course added some values in the condition column so that the test can run. At the top of the screen are two drop down tabs "analysis type" and "Summarization" The analysis type should be "Epression (Gene). I chose my summarization as RMA+DABG (All Organisms) since i am working with a miRNA4.0 chip. Then in the bottom right click "run analysis".

This brings up a new two part screen. On the left hand screen there should be three headers "Sample QC view", "Summary View", and "Gene View". Chose gene view.

This brings up a new screen. on this screen there is a drop down menu option for "Export" click on it and select the option "Export..." this brings up a new window of export options. Select "Sample Signals only" then "All rows" and then "All samples". Then click OK and it will let you export your expression table to a filename of your choice. Note that the row names will be the probeset IDs by default, if you wanted something else for your row name (such as target gene symbols, validated gene symbols, or transcriptID etc) you should, before exporting click on the 'show/hide columns option at the Gene View screen prior to export. This will add a column containing this information and you can later, I assume, use this column for your rownames when importing it in R or whatever.

There, that should do it!

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