Thalita Scandolara
de Bruijn, Ino
Hi Thalita,
Thanks for reaching out!
Could you share the link of the query you are running?
Thanks so much!
Ino
From:
cbiop...@googlegroups.com <cbiop...@googlegroups.com> on behalf of Thalita Scandolara <thalitasc...@gmail.com>
Date: Wednesday, August 30, 2023 at 11:15 AM
To: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: [EXTERNAL] [cbioportal] Problem with q-values - genomic alterations
Dear all, Hello. My name is Thalita. I am running into -what I think it is- a problem regarding the q-value results: All q-values, in exception for the first one (NSD1), have '1. 0' as a result, but I believe they are wrong. Could you
Dear all,
Hello. My name is Thalita.
I am running into -what I think it is- a problem regarding the q-value results:
All q-values, in exception for the first one (NSD1), have '1.0' as a result, but I believe they are wrong.
Could you check how these q-values are being calculated?
Thank you!
--Thalita Basso Scandolara, PhD
Doutora em Genética PGGen/UFRJ
Pesquisadora de Pós-Doutorado no INCA - Centro de Pesquisas, RJ
--
You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
cbioportal+...@googlegroups.com.
To view this discussion on the web visit
https://groups.google.com/d/msgid/cbioportal/CAHHRb8kMfRp7w2UQOd6EF84nuLfNAOpSeaAgmNTa1GXdhKzjww%40mail.gmail.com.
Please note that this e-mail and any files transmitted from
Memorial Sloan Kettering Cancer Center may be privileged, confidential,
and protected from disclosure under applicable law. If the reader of
this message is not the intended recipient, or an employee or agent
responsible for delivering this message to the intended recipient,
you are hereby notified that any reading, dissemination, distribution,
copying, or other use of this communication or any of its attachments
is strictly prohibited. If you have received this communication in
error, please notify the sender immediately by replying to this message
and deleting this message, any attachments, and all copies and backups
from your computer.
Disclaimer ID:MSKCC
de Bruijn, Ino
Hi Thalita,
Thanks for sharing the link!
I did the same test in Python using the p-values from the table. The results are the same. Only one significant result remains. There are a lot of tests performed (>18K, one for each gene), so the p-value has to be very significant for the q-value to remain significant as well
Hope that helps!
Best wishes,
Ino
From:
Thalita Scandolara <thalitasc...@gmail.com>
Date: Thursday, August 31, 2023 at 9:15 AM
To: de Bruijn, Ino <debr...@mskcc.org>
Subject: [EXTERNAL] Re: [cbioportal] Problem with q-values - genomic alterations
Hello Ino! Sure, here it is (I hope the link is right): https: //www. cbioportal. org/study/summary?id=hnsc_tcga_pan_can_atlas_2018#sharedGroups=64cffca3b01fff74fbb56a4b,64cffcd8b01fff74fbb56a4c I am comparing both groups 'ACC' and 'DEC'.
Hello Ino!
Sure, here it is (I hope the link is right):
https://www.cbioportal.org/study/summary?id=hnsc_tcga_pan_can_atlas_2018#sharedGroups=64cffca3b01fff74fbb56a4b,64cffcd8b01fff74fbb56a4c
I am comparing both groups 'ACC' and 'DEC'. Regarding the print I sent in the first email, it is the results available in the 'genomic alterations' tab.
It just seems strange to me, but if I am mistaken I apologize!
Thank you very much again!
Thalita
--