User: modarzi

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modarzi60
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Posts by modarzi

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Comment: C: Survival analysis with gene expression
... n is number of cluster. For example 3 cluster(n=3). ...
written 15 days ago by modarzi60
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Comment: C: Survival analysis with gene expression
... Dear Dr.Blighe Here you design Survival plot for 2 genes: 'MMP10' and 'CXCL12'. Suppose that we have a bunch of gene and after clustering we have n cluster. how can we design Surv plot for each cluster separately? I appreciate if you share your solution with me ...
written 15 days ago by modarzi60
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Comment: C: Survival analysis with gene expression
... Dear Dr. Blighe Really Thanks for your answer. But about my first question, I would like to explain more about my data set. It belongs to TCGA and I downloaded as UQ-FPKM. In RNA-seq analysis, this type of data set is normal. So, for using that I transformed it to Log2 space. 1- now, for using thi ...
written 21 days ago by modarzi60
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Comment: C: Survival analysis with gene expression
... Dear Dr. Blighe Thanks for your answer. I have another questions about your SA tutorial due to using RNA-seq expression data: 1-Generally, the measure of expression in RNA-seq is count and different from measure of expression in Microarray Technology. So, for using RNA-seq, Should I modify your su ...
written 22 days ago by modarzi60
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Comment: C: Survival analysis with gene expression
... Dear Dr. Blighe Thank you for this tutorial. I have a question about using `Scale()` for transforming expression data to Z scores. basically, why do we need transforming to z scores while our original data(downloaded from GEO) is normal? I appreciate if you share your comment with me. Mohammad ...
written 24 days ago by modarzi60
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Comment: C: How filter genes to construct co-expression network?
... Dear WouterDeCooster Thanks for your comment. I found another filtering strategy in an [article][1] that authors had selected genes if presented at least in 50% of samples.I mean that I have to keep genes that present at least in 50% of samples. could you please share your comment about that strat ...
written 10 weeks ago by modarzi60
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Comment: C: problem for gene survival analysis through "Survival" package in R
... all values in my last message are not real and were just for presenting my problem. but as you ask me, I would like to explain in real for you. I used WGCNA as a method for constructing my network and in my experiment I have 53 patient through 56000 gene types. so based on this method I have 62 modu ...
written 11 weeks ago by modarzi60
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Comment: C: problem for gene survival analysis through "Survival" package in R
... Dear Dr. Chris Hello, Thanks for your comment. Let me to explain more about my data in samples and patient for you. My genes profiles is data frame include N samples with M genes type as call it "mydata” based on below structure: gene1 gene2 gene3 ……. geneM ...
written 11 weeks ago by modarzi60
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Comment: C: Problem for getting P-Value in Module-Trait Relationship in WGCNA
... Dear ATpoint Hello, Thanks for your comment. You are right but in this case I have 64 modules and in some modules I have about 2000 genes. So, using 0.01 or 0.05 as cutoffs have huge different results. based on this differentiation, I read few papers for finding answer my question but up to now I ...
written 11 weeks ago by modarzi60 • updated 11 weeks ago by RamRS20k
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problem for gene survival analysis through "Survival" package in R
... Hello, My data belong to subtype of TCGA breast cancer. I have to do survival analysis for this data set. I know "survival" package but I don't know how can I involve genes profiles to survival analysis. Surly, for OS analysis, I can use "survfit" as a function for survival analysis and by "Time" a ...
R tcga survival analysis gene survival analysis written 11 weeks ago by modarzi60 • updated 11 weeks ago by raunakms980

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