User: IrK

gravatar for IrK
IrK40
Reputation:
40
Status:
New User
Location:
Australia
Last seen:
4 months ago
Joined:
3 years, 10 months ago
Email:
i*******@gmail.com

Posts by IrK

<prev • 41 results • page 1 of 5 • next >
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Comment: C: Network modeling of data produced by mixOmics (R) in Cytoscape
... I found the igraph tutorial today, will try it out :) thanks for the prompt reply. ...
written 4 months ago by IrK40
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Network modeling of data produced by mixOmics (R) in Cytoscape
... Hey guys, I'd like to visualize a network / relationships between two types of data(transcriptome data vs promote data) The network() function (Relevance Network) of the mixOmics R package suggests to save results as the graph object that can be used by Cytoscape to improve visualization. I've che ...
network mixomics multiomics cytoscape written 4 months ago by IrK40
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Comment: C: Gene-based clustering of RNA-seq data
... Thank you so much for detailed clarification, Kevin, appreciate it! ...
written 16 months ago by IrK40
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Gene-based clustering of RNA-seq data
... Hey everyone, I am trying to understand the gene-based clustering, and what strategy can be applied to see what genes fall into the same cluster based on their expression profile. I have RNA-seq data that has been analyzed with DESeq2 package for differentially expressed genes. I selected rlog n ...
clustering gene-based clustering deseq2 rna-seq written 16 months ago by IrK40 • updated 16 months ago by Kevin Blighe49k
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Cogena framework for RNA-seq / minimum sample size
... Dear Zhilong Jia, I am wondering if Cogena framework is a statistically appropriate method for co-expressed gene set enrichment analysis of RNA-seq dataset, considering that input dataset (gene counts) is appropriately normalized? What is the minimum samples number that can be used? Would 3KOs v ...
cogena tool drug repositioning pathway written 16 months ago by IrK40
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Comment: A: Differential lncRNA-mRNA co-expression
... Could you please you share the link you wanted to post ? Or kind of approach have you undertaken? Thanks ...
written 17 months ago by IrK40
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Comment: C: Gene Co-expression analysis with less number of replicates
... I have 3KOs vs 3WTs (biological replicates), WTs have to be excluded from this kind of analysis that leaves only three KO samples. So I conclude it's not possible to build coexpression network in my case as well. Very sad!!! Sounded like very interesting kind of analysis to learn. Martombo, thank ...
written 17 months ago by IrK40
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Comment: A: Gene Co-expression analysis with less number of replicates
... Hi Amol, Did you find the answer to your question? I also have three replicates and I'd like to do gene coexpression analysis, and I can't find alternative to WGCNA. Thanks ...
written 17 months ago by IrK40
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Comment: C: Goseq: Pwf: Error In If (Hi <= Low) { : Missing Value Where True/False Needed
... To be honest, I checked that NAs are absent in gene IDs vector, but forgot that numeric values also can be represented as NAs in DESeqoutput$padj vector. ...
written 2.1 years ago by IrK40
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Answer: A: Goseq: Pwf: Error In If (Hi <= Low) { : Missing Value Where True/False Needed
... I had the same error message and in my case it a binary vector had NAs, so basically: > genes = as.integer(DESeqoutput$padj <= 0.05 & > !is.na(DESeqoutput$padj)) # Give all values less than 0.05 and no NAs However, when I call for nullp() I get following warning: Can't find ...
written 2.1 years ago by IrK40

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Popular Question 2.6 years ago, created a question with more than 1,000 views. For GSEA /enrichment plot with heat map
Popular Question 2.6 years ago, created a question with more than 1,000 views. For TMM normalization for RNA seq data with three replicates (2 samples)

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