Groups
Conversations
All groups and messages
Send feedback to Google
Help
Training
Sign in
Groups
webgestalt
Conversations
About
webgestalt
Contact owners and managers
1–30 of 243
Welcome to Webgestalt user forum!
Mark all as read
Report group
0 selected
Cristian Fiorucci
,
John Elizarraras
2
Mar 14
Wrong cluster for downregulated genes
Hello, I believe this is a result of the functionality of GSEA. It doesn't necessarily care about
unread,
Wrong cluster for downregulated genes
Hello, I believe this is a result of the functionality of GSEA. It doesn't necessarily care about
Mar 14
Alessandro Chioino
Mar 14
ERROR: No IDs are mapped. Please check your input.
Hello, I am trying to run GSEA on custom database and getting the above error. Attached the
unread,
ERROR: No IDs are mapped. Please check your input.
Hello, I am trying to run GSEA on custom database and getting the above error. Attached the
Mar 14
Emeline Perthame
, …
Thanh Thanh Nguyen
4
Feb 13
Online app and R package do not return the same gene ID output with same parameters
By R package, I got 164 out of 240 unique IDs mapped to the custom enrichment category. By web, only
unread,
Online app and R package do not return the same gene ID output with same parameters
By R package, I got 164 out of 240 unique IDs mapped to the custom enrichment category. By web, only
Feb 13
Alex Saltzman
,
John Elizarraras
2
Jan 17
misaligned phospho report table
Sorry for the bug, but that should not have any affect on the data output. For those sequences, I
unread,
misaligned phospho report table
Sorry for the bug, but that should not have any affect on the data output. For those sequences, I
Jan 17
Thomas
, …
John Elizarraras
3
Jan 12
GSEA
Sorry for the delayed response. GSEA creates random permutations to create a sample population.
unread,
GSEA
Sorry for the delayed response. GSEA creates random permutations to create a sample population.
Jan 12
EZ RC
Jan 12
bugs and more bugs
terrible application
unread,
bugs and more bugs
terrible application
Jan 12
Chiara MAGRI
,
Yuxing Liao
3
12/11/23
Discrepancy between the most significant categories depicted in the gsea barchart e those reported in the enrichment result file
Thank you very much for your kind reply. Best regards Chiara Il giorno gio 7 dic 2023 alle ore 21:27
unread,
Discrepancy between the most significant categories depicted in the gsea barchart e those reported in the enrichment result file
Thank you very much for your kind reply. Best regards Chiara Il giorno gio 7 dic 2023 alle ore 21:27
12/11/23
Joris Demmers
12/5/23
'Kinase target' different requirements human vs mouse
Hi all, The requirements for the network 'Kinase target' is different for human than for
unread,
'Kinase target' different requirements human vs mouse
Hi all, The requirements for the network 'Kinase target' is different for human than for
12/5/23
Alessandro Chioino
,
Yuxing Liao
2
11/22/23
ERROR: The number of annotated IDs for all functional categories are not from 5 to 2000 for the GSEA enrichment method.
Hi Alessandro, The input is too small. Someone in the last two threads just asked the same question.
unread,
ERROR: The number of annotated IDs for all functional categories are not from 5 to 2000 for the GSEA enrichment method.
Hi Alessandro, The input is too small. Someone in the last two threads just asked the same question.
11/22/23
Sherry
11/21/23
Problem with Genenetwork to Webgestalt
Hi Guys, This is one of my first times using webgestalt so I was hoping to get some help. When I
unread,
Problem with Genenetwork to Webgestalt
Hi Guys, This is one of my first times using webgestalt so I was hoping to get some help. When I
11/21/23
Adlina Affian
, …
Alex Saltzman
4
11/21/23
Error while generating "molecular function" for Gene Set Enrichment Analysis.
If you're pre-filtering your list you should run ORA not GSEA. As stated, running GSEA on data
unread,
Error while generating "molecular function" for Gene Set Enrichment Analysis.
If you're pre-filtering your list you should run ORA not GSEA. As stated, running GSEA on data
11/21/23
ilian atanassov
,
John Elizarraras
3
11/9/23
deafferent results when using ranked list metric offset
Hello Ilian, I did a quick experiment by changing the rank offset of a list of scores . The original
unread,
deafferent results when using ranked list metric offset
Hello Ilian, I did a quick experiment by changing the rank offset of a list of scores . The original
11/9/23
isaac vingan
,
Yuxing Liao
2
10/5/23
Calculated Pvalue of 0.00000 e+00
Hi Isaac, It is from R. Basically means smaller than 2.2e-16. Yuxing On Thu, Oct 5, 2023 at 11:22 AM
unread,
Calculated Pvalue of 0.00000 e+00
Hi Isaac, It is from R. Basically means smaller than 2.2e-16. Yuxing On Thu, Oct 5, 2023 at 11:22 AM
10/5/23
Lizex Husselmann
9/28/23
Webgestalt for non-model organisms
Good Morning everybody I'm new to this field and need to functionally annotated and enrich for
unread,
Webgestalt for non-model organisms
Good Morning everybody I'm new to this field and need to functionally annotated and enrich for
9/28/23
Michael Deans
,
Yuxing Liao
3
8/11/23
ORA resulting in error message/problems with server access
Yuxing, thank you for the quick response! Changing the hostname parameter didn't work but
unread,
ORA resulting in error message/problems with server access
Yuxing, thank you for the quick response! Changing the hostname parameter didn't work but
8/11/23
Links John
,
Yuxing Liao
2
7/20/23
Inconsistent results each time
Hi, Are you doing GSEA? The nature of the permutation test will have small fluctuations. You should
unread,
Inconsistent results each time
Hi, Are you doing GSEA? The nature of the permutation test will have small fluctuations. You should
7/20/23
KJ
,
Yuxing Liao
3
7/14/23
rnk files receiving persistent error message
Thank you so much, Yuxing! I can't believe I missed them. Appreciate your help! On Friday, July
unread,
rnk files receiving persistent error message
Thank you so much, Yuxing! I can't believe I missed them. Appreciate your help! On Friday, July
7/14/23
ilian atanassov
,
Yuxing Liao
3
7/14/23
Error in startsWith(gmtFile, "http://") : non-character object(s)
Hi, It is probably because you mean interestGeneType="genesymbol" instead of
unread,
Error in startsWith(gmtFile, "http://") : non-character object(s)
Hi, It is probably because you mean interestGeneType="genesymbol" instead of
7/14/23
marianna rossi
,
Yuxing Liao
2
7/6/23
upload gene list
Hi Marianna, The file is expected to have two columns with a tab separating them. Could you attach an
unread,
upload gene list
Hi Marianna, The file is expected to have two columns with a tab separating them. Could you attach an
7/6/23
alessio colantoni
, …
Yuxing Liao
5
7/3/23
Organism not found
Hi, could you try again? There was a problem with the server earlier today. Yuxing On Mon, Jul 3,
unread,
Organism not found
Hi, could you try again? There was a problem with the server earlier today. Yuxing On Mon, Jul 3,
7/3/23
NY
6/16/23
Hi, why negative enrichment of some GO on volcano plot in ORA?
Hi, why negative enrichment of some GO on volcano plot in ORA?
unread,
Hi, why negative enrichment of some GO on volcano plot in ORA?
Hi, why negative enrichment of some GO on volcano plot in ORA?
6/16/23
Alex Saltzman
,
Yuxing Liao
3
5/18/23
option to permute by gene_set for calculating FDR?
Hi Alex, I think because we run preranked GSEA. It should permutate by gene set. Understand and keep
unread,
option to permute by gene_set for calculating FDR?
Hi Alex, I think because we run preranked GSEA. It should permutate by gene set. Understand and keep
5/18/23
Daniel Levis
,
Yuxing Liao
4
4/19/23
Genes not mapped
I would say the annotations of non-coding genes are still sparse. Even if we used Ensembl gene ID
unread,
Genes not mapped
I would say the annotations of non-coding genes are still sparse. Even if we used Ensembl gene ID
4/19/23
InesH
,
Yuxing Liao
2
4/17/23
use of reference gene list in GSEA
No, you can think GSEA uses the input itself as the reference. The statistics is based on
unread,
use of reference gene list in GSEA
No, you can think GSEA uses the input itself as the reference. The statistics is based on
4/17/23
Xunzhi Zhang
4/15/23
Genes with the same rank metrics in GSEA
Hello, In GSEA, genes are ranked based on their rank metrics from the input. I wonder how WebGestalt
unread,
Genes with the same rank metrics in GSEA
Hello, In GSEA, genes are ranked based on their rank metrics from the input. I wonder how WebGestalt
4/15/23
Cristian Fiorucci
,
Yuxing Liao
2
3/24/23
Visualization error
Hi Cristian, Could you share an example link? Thanks. Yuxing On Fri, Mar 24, 2023 at 3:25 AM Cristian
unread,
Visualization error
Hi Cristian, Could you share an example link? Thanks. Yuxing On Fri, Mar 24, 2023 at 3:25 AM Cristian
3/24/23
Cristian Fiorucci
,
Yuxing Liao
3
3/16/23
Different significance with ORA and GSEA
Thank you for your help! Il giorno mercoledì 15 marzo 2023 alle 21:22:19 UTC+1 yuxin...@gmail.com ha
unread,
Different significance with ORA and GSEA
Thank you for your help! Il giorno mercoledì 15 marzo 2023 alle 21:22:19 UTC+1 yuxin...@gmail.com ha
3/16/23
Letoto H
,
John Elizarraras
6
3/15/23
rnk files
The order of the genes does not matter, but they should all have a score. Happy to help, and if you
unread,
rnk files
The order of the genes does not matter, but they should all have a score. Happy to help, and if you
3/15/23
Juan Manuel Luque
,
Yuxing Liao
2
3/13/23
To change colors of Bar chart
Hi Juan, Sorry, your email went to spam. For the question, unfortunately you can't on the website
unread,
To change colors of Bar chart
Hi Juan, Sorry, your email went to spam. For the question, unfortunately you can't on the website
3/13/23
Mario Ezquerra
,
Yuxing Liao
2
2/16/23
Uniprot protein ID with phosphosites annotation format?
Hi Mario, There are 4 ID types, and hovering over the options after a while shows a few examples. You
unread,
Uniprot protein ID with phosphosites annotation format?
Hi Mario, There are 4 ID types, and hovering over the options after a while shows a few examples. You
2/16/23