User: Chanchal Kumar

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Posts by Chanchal Kumar

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Comment: C: How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrez
... Hi Anna, I am sorry to not mention this before but by fold change I meant the following, fold change = ratio(treated with stimuli / non treated control). And for OMIM I have decided to create my own annotation package as that’s much easier to use. Best Regards, Chanchal ================= ...
written 10.8 years ago by Chanchal Kumar130
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Answer: A: How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrez
... Hi Anna, Thank you for the reply. As the GSEA(from Broad Institute) has an option for analyzing preranked list of genes so I was curious if similar functionality exists in Bioconductor as well. I will like to use GSEA to get the OMIM etc. related information using Bioconductor as I don’t thin ...
written 10.8 years ago by Chanchal Kumar130
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How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?
... Dear All, I have a set of Entrez ids which have been ordered as per fold change expression from a control experiment. I am now interested in carrying out gene set enrichment analysis using Bioconductor GSEABase package. I don't have any other statistics for these genes. Is it possible to carry ou ...
proteomics hgu95av2 gseabase written 10.8 years ago by Chanchal Kumar130
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Comment: C: Inconsistency in GOstats results after GO enrichment
... Hi Robert, That peculiar p-value was for the sake of reproducing my concern which has eventually turned out to be an algorithmic implication due to conditional testing. And at that time was chosen to just get some GO terms which were common but having different category sizes. I totally agree w ...
written 11.2 years ago by Chanchal Kumar130
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Answer: A: Inconsistency in GOstats results after GO enrichment
... Hi Tony, James and All, This mail is to inform you that this issue is now cleared. As per what I have been conveyed by Robert Gentleman through James the explanation is as follows: The conditioning has to happen on both the GO terms for the selected genes as well as for the GO terms from the u ...
written 11.2 years ago by Chanchal Kumar130
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Inconsistency in GOstats results after GO enrichment
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080229/ e5473ce3/attachment.pl ...
written 11.2 years ago by Chanchal Kumar130 • updated 11.2 years ago by James W. MacDonald50k
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Comment: C: How to retrieve environment variables from custom build annotation packages
... Dear Dr. Huber, Thank you very much for your suggestion. It really helped. Best Regards, Chanchal =============================== Chanchal Kumar, Ph.D. Candidate Dept. of Proteomics and Signal Transduction Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 D-Martinsried (near Muni ...
written 11.4 years ago by Chanchal Kumar130
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How to retrieve environment variables from custom build annotation packages
... Dear Bioconductor Developers and Users, I have a custom annotation package which I created using "AnnBuilder" package. The package named "ipihs324" has annotation for IPI identifiers and contains mappings to Entrez ids in the environment variable ipihs324ENTREZID. Now when I provide this enviro ...
proteomics annotation convert written 11.4 years ago by Chanchal Kumar130 • updated 11.4 years ago by Wolfgang Huber13k
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Comment: C: Query about the conditional hypergeometric test in GOstats package
... Dear Dr. Gentleman, Thanks for the inputs. It was indeed helpful and now after reading the references the concept is pretty clear. Best Regards, Chanchal =============================== Chanchal Kumar, Ph.D. Candidate Dept. of Proteomics and Signal Transduction Max Planck Institute of Bioche ...
written 11.5 years ago by Chanchal Kumar130
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Comment: C: Query about the conditional hypergeometric test in GOstats package
... Dear Jim, Thank you very much for the information. It was indeed very helpful. Now I did my analysis with the "conditional" argument as TRUE and I see that the result is more explainable. I am thinking of using this conditional test in rest of my analysis. I will go through the reference as wel ...
written 11.5 years ago by Chanchal Kumar130

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