There are several areas that have caused trouble to researchers previously, including:
Permissions. Some data, particularly identifiable genetic data, must be used on the RAP and not downloaded. Older projects that are Tier 0 can use the RAP but their access permissions are controlled by what data has been approved in a Basket.
Size of the data and lack of space on the receiving computer.
Size of the data and speed of the intervening networks.
Data that is incomplete on the platform.
Could you describe what data you are trying to download, what commands you are using, and what problem you are seeing.
Firstly, am on Tier 0, my variable is 21 in number, it consists of sociodemographic data, dietary intake and diseases. what options can I use to analyze my data? thank you for your assistance.
Application 80300 is currently a Student-Tier (tier 12) project. Student-tier projects need to process the data on the RAP, and not download the data at all.
If you only need 21 variables, I suggest you use the cohort browser to select the variables you need, and to filter for the participants you need. Save that table to your main project file storage. Open a JupyterLab instance. Open a Notebook, and run either python commands or R commands on that saved table. Ensure that you save all results back to the main project file storage before you close the instance.
An alternative would be to open a Spark JupyterLab instance. This is larger, and can hold the whole of the tabular phenotypic data, so there is no need to pre-select your variables.
Thank you Rachael W el. i have been able to work my way around this,. However, I have seen a lot of resources regarding using STATA on Jupyter Lab. I have tried to set up my Stata 18 on Jupyter. Have you used STATA o Jupyter before or do you a link to any video that will be of help? Thanks for your anticipated assistance. Rachael W hael ?
Application ID 81793 is a Student-tier project. Student-tier projects need to process all data on the RAP, and not download the data at all.
To see whether their project is Student-tier, researchers can look at Annex 4 of their copy of the Material Transfer Agreement, MTA, and follow the link in blue which says "Approved project details", and look under "Specific Conditions" to see whether it says "Approved for reduced student fee".
Of course, you will eventually need to download the derived results of your analysis, and this is expected. These results should not include any participant-identifiable data. If you are still unsure whether your results may be downloaded, please ask again here in more detail, or contact the access team by email directly.
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There are several areas that have caused trouble to researchers previously, including:
Could you describe what data you are trying to download, what commands you are using, and what problem you are seeing.
Thank you for your reply
Firstly, am on Tier 0, my variable is 21 in number, it consists of sociodemographic data, dietary intake and diseases. what options can I use to analyze my data? thank you for your assistance.
What is the Application ID for the project?
The application ID is 80300
Application 80300 is currently a Student-Tier (tier 12) project. Student-tier projects need to process the data on the RAP, and not download the data at all.
If you only need 21 variables, I suggest you use the cohort browser to select the variables you need, and to filter for the participants you need. Save that table to your main project file storage. Open a JupyterLab instance. Open a Notebook, and run either python commands or R commands on that saved table. Ensure that you save all results back to the main project file storage before you close the instance.
An alternative would be to open a Spark JupyterLab instance. This is larger, and can hold the whole of the tabular phenotypic data, so there is no need to pre-select your variables.
For more information on using the cohort browser, see https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/working-with-ukb-data#browsing-dataset-fields-using-the-cohort-browser
For more information on using JupyterLab, see https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/using-jupyterlab-on-the-research-analysis-platform
Thank you Rachael W el. i have been able to work my way around this,. However, I have seen a lot of resources regarding using STATA on Jupyter Lab. I have tried to set up my Stata 18 on Jupyter. Have you used STATA o Jupyter before or do you a link to any video that will be of help? Thanks for your anticipated assistance. Rachael W hael ?
Hello Rachael W ?,
Where can I find out exactly of which data is downloadable or must not be downloaded in my project? My Application ID is 81793.
Hi {@005t000000BBrFkAAL}?
Application ID 81793 is a Student-tier project. Student-tier projects need to process all data on the RAP, and not download the data at all.
To see whether their project is Student-tier, researchers can look at Annex 4 of their copy of the Material Transfer Agreement, MTA, and follow the link in blue which says "Approved project details", and look under "Specific Conditions" to see whether it says "Approved for reduced student fee".
The UKB fee structure is at https://www.ukbiobank.ac.uk/enable-your-research/costs .
Of course, you will eventually need to download the derived results of your analysis, and this is expected. These results should not include any participant-identifiable data. If you are still unsure whether your results may be downloaded, please ask again here in more detail, or contact the access team by email directly.
I haven't used Stata at all, sorry, so I am not able to help with this.
Hi Rachael W ? ,
Thank you so much for your detailed response. I will send an email to access team.
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