Analysing user data on Genome Wide Association Study


1) What page is the analysis page?
2) What is required to run the analysis?
3) What is the correct format for the text file from a user?
4) What are the steps involved in the analysis?
5) The problem started when I clicked on the Upload button?
6) The problem started when I clicked on the Run button?
7) How can I find out more about ALSoD?



1) What page is the analysis page?

To access the analysis page, a username and password are required for security reasons.
The analysis starts at http://alsod.iop.kcl.ac.uk/charts/chisquareindex.aspx 
And the general page is http://alsod.iop.kcl.ac.uk/GWA2/index.aspx 

2) What is required to run the analysis?

Apart from a username and password which is given to every user after registartion, a text file containing the user's data is also required in the correct format.

3) What is the correct format for the text file from a user?

The correct and acceptable format for the text file is the plink format but without headings

1) There MUST be four (4) columns : CHROMOSOME, SNP, POSITION, P-VALUE
2) Each field or column should be seperated with TABs
3) No headings on the first row
4) After the P-Value, there should only be return to the next line and not another TAB
5) On the last row, the cursor must stop at the end of the P-value column
6) Column specification:
CHROMOSOME - Integer
SNP - String (Alphanumeric)
POSITION - Integer
P-VALUE - Float (with decimals)
7) You can export file from plink but remember to edit the text file by removing the first line(heading)
8) The text file must be with a .txt extension and nothing else


4) What are the steps involved in the analysis?

There are three simple steps to analyse your data:
1) Upload data - to insert text file to database
2) Run Analysis - to run scripts
3) View Graph - to display chart of the combined p-values

5) The problem started when I clicked on the Upload button?

1)This indicates that there must be a problem with the text file you are uploading so check the format properly or
2)Another user is carrying out an analysis at the same time as you so you need to exercise patience and wait... for about an hour
3)If the problem persists, please send an email to the Administrator with your attached text file

6) The problem started when I clicked on the Run button?

Click on   to debug the error  This may take a few minutes please be patient   

7) How can I find out more about Alsod?

Please contact Olubunmi Abel on +44(0)2078485244 for details