This page gives some answers to questions that (we think) will be frequently asked about the upload section.
Q: What is the meta-analysis webpage used for?
A: In order to perform a meta-analysis, we need each group to upload the statistics of association for each marker from their GWAS studies. In addition, we need a good deal of demographic, study design, and quality control information. Please do not upload any raw genetic data or neuroimaging data. The meta-analysis works specifically on the results files from the GWAS analysis.
Q: Why are there so many boxes to fill out?
A: There is a lot of information being requested so that (1) we have descriptive statistics of each sample, (2) we can check that the information is in general consistent across groups, and (3) we can publish these results quickly and efficiently.
Q: What should I do when it asks me that Java wants to run something from this page?
A: Please allow Java to run on the webpage. The upload utilities for the large GWAS results files are Java based. They will split up the files you are uploading into multiple small chunks that can be efficiently transferred to the servers at LONI. If you do not have Java on your machine, please download it here: http://www.java.com/en/download/index.jsp.
Q: Can I upload from a computer of using Windows/PC/Linux?
A: Yes, the only special program you need is Java which is most likely already installed on your machine. If not though, please download it here: http://www.java.com/en/download/index.jsp.
Q: Can I save information I enter on this form before I have finished entering it all?
A: The meta-analysis section will save whatever you enter as soon as you hit the Submit button at the bottom of the page. When you login, it will automatically pull up your information, which you are are free to edit. In the Analysis sections, you can only attach one image. If you hit "Browse" and select a new chart/image from your local folder, then it will replace the former.
Q: How do I describe imaging QC failures?
A: An example QC failure description is: right hippocampus delineation failed.
Q: How do I make the histograms and boxplots?
A: Please see the extensive protocols on this website.
Q: I used different SNP exclusion criteria than those listed on the upload page. How do I convey this to the meta-analysis group?
A: Please specify the exclusion criterion you used in parentheses after the number of SNPs excluded.
Q: How long will it take to upload?
A: It should take < 10 minutes per upload box depending on your internet speed and distance from Los Angeles.
Q: My results are on a Linux server and I use a Mac/Windows computer to browse the internet. How do I drag and drop?
A: You can either (1) use an FTP client to transfer the files from your Linux server to your local machine and then drag and drop into the webpage, (2) mount your Linux server to your local machine using a Samba server client, or (3) remotely log in to your linux server, open a browser, and drag the file from the Linux side.
Q: How do I know if my upload is complete?
A: After you drag and drop the information into the box, it will give something like the result below. Make sure that however many chunks it says it created are actually being created (in this case 13), and that the box says Upload completed for the final chunk. It will lag with the final completion message because it is putting the file back together.
Q: How do I know the meta-analysis group successfully received my results?
A: You will receive an email from the meta-analysis group if there is any trouble or to confirm that all your data is uploaded successfully and will be ready to use in the meta-analysis.
Q: If I used a different association program than mach2qtl, how do I upload the results?
A: Any association program that accounts for the probabilistic nature of the imputed SNPs during association is ok to use. You should have one text file per GWAS or one per chromosome per GWAS. Either way the file(s) should be compressed through tar and gzip prior to uploading.
Q: I only have healthy subjects in my analysis, what do I do about all the boxes which involve patients?
A: You can leave them blank.
Q: I'm confused, who do I contact to help?
A: Please email enigma@lists.ini.usc.edu for help.
