Genomestudio: The Project Can Not Be Created. No Valid Samples Were Loaded

Question

[Click downvote]

What does this error message tell me?

I do

1. "New Project"
2. Then I select an appropriate name
3. Then I choose "Use sample sheet to load sample intensities."
4. Then I select the appropriate sample sheet.
5. On the same page I also select the Data repository and Manifest repository. I let these be the same folder as the one where my data files are stored.
6. Then I click Finish (I've tried this last step both using and not using the import cluster positions option.

Then I get a GenomeStudio Progress Status window that says first

Loading Manifest <name removed="">, then Loading 9275091022,R01C01, but eventually this stops and I get an error window with "The project can not be created. No valid samples were loaded".

I'm thinking the error might occur because of step 5. I do not know what these path values are supposed to be.

Another possible source might be the sample sheet I load.

The head of it looks like:

[Header],,,,,,,,,,,,,,
Investigator Name,SEE,,,,,,,,,,,,,
Project Name,2012_2645_Gen-sepsis,,,,,,,,,,,,,
Experiment Name,2012_2645_Gen-sepsis,,,,,,,,,,,,,
Date,04/07/2013,,,,,,,,,,,,,
[Manifests],,,,,,,,,,,,,,
A,humancoreexome-12v1-0_b,,,,,,,,,,,,,
[Data],,,,,,,,,,,,,,

Seems like the are some fields not filled out like Manifests and Data. Can this be relevant?

[curious]

I am going through the same thing and finding the GUI a bit challenging. I am trying to update with some comments to help others as much as possible. What got me past this error is that the suffix of files need to be RED and GRN. Red and Grn will not work. Reading the error log at the bottom console on genome studio had been helpful.

Answer 1

[Charles Warden]

I don't think you need the sample sheet.

Getting data into Genome Studio was initiallly a little tricky for me because it required a specific file structure.

If the ID on your chip is "9275091022", you need to include all of the .idat files within a folder with that same ID. If you have multiple IDs, you need multiple input folders. It is OK if your project only used a portion of the slots available on a particular chip.

You may also need a file to specify the chip design, but I think that is the last step.

If you need detailed help, you can contact Illumina: [e-mail]

[Ying W]

also make sure that all the *.idat files are there since those are the files that genome studio will read in

[Click downvote]

The only thing I was supposed to use was bmp and egt files, at least according to the technical note published by Illumina: http://res.illumina.com/documents/products/technotes/technote_infinium_genotyping_data_analysis.pdf However, I see that there are a number of idat files in our folders. Will have to try to include those.

[Click downvote]

This seems like a better guide: http://supportres.illumina.com/documents/myillumina/d2c2c169-36c7-4613-89d6-bf34588a7624/genomestudio_gt_module_v1.0_ug_11319113_reva.pdf

[Ying W]

ahh my bad, I was thinking Genome Studio for expression data, btw nice username :P

Answer 2

[Philipp Bayer]

I just ran into this error when connecting to a Windows machine via remote desktop connection from a Linux (Fedora system). The data was stored on the Linux system while GenomeStudio ran on the Windows machine.

Copying the data onto the Windows machine before loading it into GenomeStudio made this error disappear.

Answer 3

[shenzhongjun]

In addition to the suggestions provided by everyone above, I add that you should check whether the .bpm file and .egt file used match your chip. I also encountered this problem when I used the manifest file of the ASAMD chip to analyze the data of the ASA chip.