Hello,
I was running analyses on ecotoxxplorer, and noticed the gene H6PD would be tagged ** despite being 0.066. Is this normal / is it because it’s close to 0.05?
Thanks for letting us know, the cut-off for flagging housekeeping genes was recently changed from 0.1 to 0.05. We had changed the cut-off in the calculation part, but not the plotting function. I’ve updated and the change should be live soon.
Just to check - the p-value 0.066 was starred in the plot, but the “Housekeeping genes” quality check was not flagged, right?
Hello Jess,
Thank you for fixing the issue!
Yes, despite looking significant while plotted, it didn’t get flagged during the hkg check.
Hello Jess,
Happy New Year! I hope you’re well 
I was analyzing some samples on EcoToxXplorer and one of the housekeeping genes was flagged again despite being > 0.05 (it was 0.08). I included a screenshot. The issue may not have been permanently resolved from last time.
Hi
Can you provide a copy of your data and I will look into it? When I try the example data that has one HKG p-value of 0.083, it is correctly not being flagged:
You can also try clearing your browser cache and trying again - sometimes changes we make on our end are not available until you do this.
Hello Jess,
Apologies hadn’t seen your message.
For sure, thank you for looking further into the matter! I can only upload 5 files at a time to this reply, so instead I’ve put them in a drive folder that has all the files in it that you should be able to access and download:
https://drive.google.com/drive/folders/1BqOG0tPZ9ANCLnAKS23_luv-c5RwGijp?usp=sharing
CTRL files are the controls, and A to F are progressively increasing doses, and there’s 5 replicates per dose and control group. Let me know if you have any issues accessing it I can send them to you be email instead. Mine is Ramela.koumrouyan@mail.mcgill.ca
Thanks in advance,
Ram
Hi Ram,
I’m not sure what’s happening on your end - when I run these samples the plot is only flagging the one less than 0.05:
It’s extremely weird if you are still getting 0.08 flagged after re-running now. Is there any way that image could be from old results? If running again, make sure to clear your cache. Cache shouldn’t matter for this type of thing, but I can’t think of any other reason.