GSEA, ssGSEA, and ssGSEA-ROC. Please, I would like to know whether I can run those analyses with the expression dataset in pmeTPM format directly or whether I should first normalize

the online ssGSEA GenePattern module.* I have 4 samples (4 sample columns)* I formatted the gene expression file according to GSEA requirements for .gct files first in excel. Then

> the ssGSEA "2.0" or GSVA algorithms have made, they're a 3rd parties that > have adapted the core ssGSEA algorithm that we developed for additional > purposes

in the ssGSEA or GSEA algorithm. It's possible that you're just using a different term than we do, so if you could point me to whatever documentation has driven these questions

bad, ssGSEA is actually located in the GSEA org repository not the GenePattern resposiotry, sorry about that! Here's the link: https://github.com/GSEA-MSigDB/ssGSEA-gpmodule

using the ssGSEA module when my results could not be > downloaded.How can I fix it?[image: 1.png] > > -- > You received this message because you are subscribed to the Google

Anthony, ssGSEA worked! >> >> I'm now trying to visualize the results using the ConstellationMap >> module. To do this, I first created a cls file with ClsFileCreator

to run ssGsea after collapsing the dataset. On Thursday, August 1, 2024 at 5:00:10 PM UTC+1 Anthony Castanza wrote: > Hi Kudzayi, > > It looks like your dataset is using Ensembl

happening with ssGSEA to more users than just you. > Jobs being submitted with the default settings (2GB RAM in particular) are > all failing this way. Resubmitting the job requesting

to run ssGSEA using RNA expression data that lacks a > value for a particular gene for a specific sample? > > Thanks, > Jane > > -- > You received this message because

, however ssGSEA has a hard coded internal gene set size of maximum 2000 genes. We suggest to restrict the gene list further by going back to the source data and restrict the potential

Module: ssGSEA >>>>> urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00270:10.1.0 >>>>> # Parameters: # input.

this through ssGSEA where such a transform would be > repeated. That said, I'm not a statistician, so I would probably recommend > consulting with one in this case if your

order for ssGSEA to be able to parse the file it > needs to be saved out of excel as tab delimited text (.txt), and only then > renamed to the .gmt file extension. Once you've corrected

>> ssGSEA.ROC that is available through GenePattern. If you have questions >> about how the procedure works, please let me know. >> >> >> >>

like the ssGSEA docker container is either dying or else gets into an endless loop trying to get enough memory to run. Is there a reason not to just use the public server since you already

taskLib/ssGSEA.10.1.0.1/ssGSEA.R file. So there >>> are a few things to check. >>> >>> 1. Is the server's tasklib available outside of the server

run the ssGSEA ROC module and am receiving the > following error: > > Error in parse(text = paste0("dataset$", > dataset_calculations[dataset_calculations

difficulties running ssGSEA   hello, I am trying to run ssGSEA, but am encountering the following error: Error in vector(length = gene.set.size, mode = "character") : invalid

in the ssGSEA implementation on GenePattern. > > In order to show and remove this extra file extension you'll need to > enable your operating system's option to "

try running ssGSEA again after changing the identifiers in the GMT file to match the identifiers in the GCT file. Example: in the GMT file, there is the identifier: LDGENIYIRHSNLM-

to run ssGSEA on the GenePattern server: https://cloud.genepattern.org/gp/pages/index.jsf?lsid=urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis

, where ssGSEA is operating assuming US > decimal formatting. > > Regards, > David > > David Ebywww.gsea-msigdb.orgigv.org > genepattern.org > > >

variants like ssGSEA are designed to use the information for all expressed genes as the input, then from within that the overrepresentation of a subset (gene set) is tested. Utilizing

Calls: ssGSEA.cmdline >> Execution halted" >> >> >> On Wed, Oct 26, 2022 at 6:56 PM Vithurran Thavarajah < >> vithurran.thavarajah@gmail

Hi Mario, Quick follow up. I have a workaround for you. If you change the names of your gene sets to replace the "-" with "_" the

file. ssGSEA computes enrichment at both the top (positive scores) and bottom (negative scores) of the input expression data. -Anthony Anthony S. Castanza, PhD Curator, Molecular

in the ssgsea module. I have >>> checked that the number of samples/columns is 6658. So I am not sure of the >>> source of the error. Please let me know. >>>

sure that ssGSEA is able to work on copy number or > methylation data. To answer this I suggest you ask the GSEA experts at > https://groups.google.com/group/gsea-help. >

trying a ssGSEA but it constantly appears the following error: There > was an unexpected file transfer error while submitting your job. Please > check your network connection