Dear all,
im using Illumina's HT-12 v4 Expression BeadChip, and i'd like to know if it is possible to get raw expression data files from the Illumina iScan system without the need to use GenomeStudio to generate those. I've learned that the ".idat"-format is proprietary and encrypted. So: is it possible to configure the iScan system to directly output unencrypted .txt files - or even better: bead-level data - just like with the older BeadScan system (via settings.xml)? And if so, how? The iScan manual file on the Illumina homepage is not accessible (at the moment), and I can't find any hints on the net.
Yours, Daniel
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As far as I know there's no way to turn the encryption off for the expression idat files. However, they can be read using the R package available here:
http://www.compbio.group.cam.ac.uk/software/idatreader
If you don't want to use R for the analysis you can write the decrypted file back to a tab delimited file.
Thank you for your quick answer. I'll try that tomorrow.
But just to clarify: are the .idat files really encrypted? I mean, if they were, you couldn't just decrypt them without using any kind of password. So would it be more correct to say that they are simply in a weird proprietary format, one that can be read by "idatReader"?
Yours, Daniel
They really are encrypted, using the DES algorithm. That's why IDATreader requires certain C libraries to be available, it uses the decryption routines implemented in either of those libraries.
Once the file has been decrypted it's in an proprietary XML format, which is then parsed to generate a table of the data.
You don't need to worry about a password or anything. A key is required, but it seems to be consistent for all expression idats. If you dig through the source code of the package you can find it.
No, the iscan system does allow bead-level data. I have been provided it by a number of groups and would actively encourage anyone using the BeadArray platform to try to get hold of it. Unfortunately, I don't have access to a machine myself, I've been hoping someone else could provide the details of how to obtain it. I had assumed it was still done by editing the settings.xml file. Illumina's FAQ (Question 27) simply says to contact tech support: http://www.illumina.com.cn/support/faqs.asp
So Illumina tech support got back to me with the following instructions for obtaining bead-level data. I don't have access to an iScan machine, so if anyone could reply with whether it was successful or not, that would be great.
Thank you for your request. Luckily, collecting bead level data on an iScan is much easier than on a BeadArray reader.
-After launching the iScan Control Software, go to the Menu Arrow at the top left and Options.
-Select Scan settings, go to the scan settings file for your beadChip product and create a copy using the Copy button at the bottom of the window (Note: original scan setting files cannot be modified!).
-Name the new Scan Settings (.scst) file with a name reflecting that it is collecting Bead level data (e.g. InfiniumHDbeadlevel.scst) and save.
-Click on the new file you created under Scan settings. Under Analysis make sure that ‘Include Outliers’ is set to ‘true’ if you want to collect data from every bead, or ‘false’ if you would not like to collect outlier beads.
-In the Output section, you will define whether or not you wish to ‘Export Bead Data’ which means exporting a text file with intensity values for each individual bead. In this case, we want to set this to ‘true’. Export Bead Type data = True will give a text file indicating the average bead intensity for each Bead Type. You can also define whether or not to ‘Include XY in Bead Data’. This will indicate whether X, Y pixel coordinates will be saved in the Bead Data file if Export BeadData is set to ‘true’. Set this option to ‘true’. Before starting the scan, please make sure to point to the new scan settings, not the default scan settings file.
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