User: miky.zo

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miky.zo40
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New User
Location:
Italy / Busto Arsizio / University of Insubria
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1 week, 2 days ago
Joined:
6 months, 2 weeks ago
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m*************@gmail.com

Posts by miky.zo

<prev • 18 results • page 1 of 2 • next >
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Comment: C: How to export molecular action between nodes from String PPI network?
... Thank you for your answer! I am trying to export the network in cytoscape; is there a way to then import this information (molecular action) into the network inside cytoscape? ...
written 26 days ago by miky.zo40
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Comment: C: Combining GSEA (Gene Set Enrichment analysis) and DEG (Differentially Expressed
... You're right, sorry, I wrote something that can create confusion: with DEG list I mean the list that you obtain after you analyze your two conditions in the RNAseq/microarray, so technically they are just the genes that come out from analysis with pval and logFC. :) ...
written 26 days ago by miky.zo40
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Comment: C: Combining GSEA (Gene Set Enrichment analysis) and DEG (Differentially Expressed
... Hi! I don't understand how you would do a GSEA without having a list of Differentially Expressed Genes... What would you insert as input in the analysis? The GSEA starts with a list of DEGs, so in any case you need to do it beforre running GSEA. So, you do DEG analysis and find genes up regulated ...
written 27 days ago by miky.zo40
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Answer: A: Combining GSEA (Gene Set Enrichment analysis) and DEG (Differentially Expressed
... Hi @chokevin8, I think that there is a misunderstanding in the methods. You use the GSEA method to analyze your DEGs list (or at least, is what I understood GSEA exists for). So, you can first find your DEG list, with gene name/symbol/ID, pvalue and log FC. Then you use this list to run a GSEA. Als ...
written 29 days ago by miky.zo40
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How to export molecular action between nodes from String PPI network?
... Hi everybody. I am using the online version of STRING (https://string-db.org) to build a PPI network using DEGs from RNAseq analysis. In the settings, I checked the "molecular action" box to visualize the predicted mode of action for the interaction between different nodes. But when I export the . ...
systems biology bioinformatics ppi string network written 4 weeks ago by miky.zo40 • updated 26 days ago by Jean-Karim Heriche23k
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Answer: A: DNA methylation integrated package
... Hi! I suggest, if It's possible, to find a bioinformatician that can do it for you or learn by yourself how do to it using R programming and bioconductor. In a similar topic (https://www.biostars.org/p/432297/#432322) I suggested an user to follow this tutorial: https://www.bioconductor.org/packages ...
written 4 months ago by miky.zo40
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Comment: C: How to do Disease-Free survival analysis with TCGA data ??
... Ok, I'll try pfs, thank you! ...
written 4 months ago by miky.zo40
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Comment: C: How to do Disease-Free survival analysis with TCGA data ??
... Hi, thank you for your answer! The problem is that in PRAD, there are very few death events (like 10 in 500 cases) so I don't think that doing overall survival will give good results with this dataset, so I thought that DFS might be better. ...
written 4 months ago by miky.zo40
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How to do Disease-Free survival analysis with TCGA data ??
... Hi everybody! I am trying to do survival analysis with TCGA-PRAD data. I learned how to do overall survival, KM plots and cox regression following this tutorial: https://bioconnector.github.io/workshops/r-survival.html , in which you learn how to use R packages "survival", "survminer" and TCGA data ...
disease-free survival R tcga survival analysis written 4 months ago by miky.zo40 • updated 4 months ago by MatthewP690
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Answer: A: Appropriate Pipeline for Methylation EPIC array analysis?
... Hey, I am kinda new to this field but I had to do some analyses on an EPIC array. I followed this R cross-package tutorial for methylation analysis: https://www.bioconductor.org/packages/release/workflows/vignettes/methylationArrayAnalysis/inst/doc/methylationArrayAnalysis.html , I think you will fi ...
written 4 months ago by miky.zo40

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