Posts

Showing posts from September, 2021

Uploading data to GEO - which method is faster?

Image
If you have had to upload omics data to GEO before, you'll know it's a bit of a hassle and takes a long time. There are a few methods suggested by the GEO team if you are using the Unix command line:   Using 'ncftp' ncftp set passive on set so-bufsize 33554432 open  ftp://geoftp:yourpasscode@ftp-private.ncbi.nlm.nih.gov cd uploads/your @mail.com_ yourfolder put -R Folder_with_submission_files Using 'lftp' lftp  ftp://geoftp:yourpasscode@ftp-private.ncbi.nlm.nih.gov cd uploads/ your @mail.com _ yourfolder mirror -R Folder_with_submission_files Using 'sftp'  (expect slower transfer speeds since this method encrypts on-the-fly) sftp  geoftp @s ftp-private.ncbi.nlm.nih.gov password: yourpasscode cd uploads/ your @mail.com _ yourfolder mkdir new_geo_submission cd new_geo_submission put file_name Using 'ncftpput'  (transfers from the command-line without entering an interactive shell) Usage example: ncftpput -F -R -z -u  geoftp  -p "yourpasscode&q

Urgent need for minimum standards for reproducible functional enrichment analysis

Image
So our preprint is online called “ Guidelines for reliable and reproducible functional enrichment analysis” so I thought I’d give you an overview . Enrichment analysis is widely used for exploration and interpretation of omics data, but I’ve noticed sloppy work is becoming more common. Over the past few years I’ve been asked to review several manuscripts where the enrichment analysis was poorly conducted and reported. Examples of this include lack of FDR control, incorrect background gene list specification and lack of essential methodological details. In the article we show how common these problems are and what the impact could be on the results. In this article we did two screens of articles from PubMed Central. Firstly selected 200 articles with terms in the abstract related to enrichment analysis. These were examined with regards to a checklist around reporting and methodological issues, and were cross-checked for accuracy. As some articles describe >1 analysis, the total numbe