User: modarzi

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modarzi80
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Posts by modarzi

<prev • 105 results • page 1 of 11 • next >
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Problem for downloading Non-coding RNA from Gene Expression Omnibus (GEO)
... Hi, I want to download Non-coding RNA profiling by high throughput sequencing from GEO. My favorite data set is GSE114327. In that data set in Supplementary file section, I download just one of the file by clicking on the custom section from GSE114327_RAW.tar. After extracting the file, I open “GS ...
geo non-coding rna written 3 days ago by modarzi80
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Comment: C: how to filter genes in significant module?
... Hi, my origin number of genes in the dataset is 3000 and after constructing, I find 9 modules as I said in the privous comment. The 1501 genes are high in a turquoise module. I would like to achieve a fewer number of genes for finding better results. I use cutreeDynamic() for Module identification b ...
written 10 days ago by modarzi80
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finding Topological Overlap Matrix(TOMType) value in TOMsimilarity() function in WGCNA
... Hi, based on constructing Co-expression network by "signed hybrid" as a network type I need a guide for TOMsimilarity() function. In that function, one of the arguments is TOMType which specifying TOM type to be calculated. So, should be TOMType same as "Network Type"? I mean when I selected "s ...
wgcna tom written 10 days ago by modarzi80
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how to filter genes in significant module?
... Hi, I used WGCNA for finding modules. I found 9 modules: turquoise(1501), red(173), pink(41), magenta(36), grey(6), green(446), brown(348), blue(382),black(67). Based on Univariate Cox Model just turquoise is significance. The number of 1501 genes in turquoise module is high and I have to filter mo ...
wgcna significant modules written 10 days ago by modarzi80
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Comment: C: Survival analysis with gene expression
... Thanks, Dr. Blighe. I solved my problem but in the below code: ggsurvplot(survfit(Surv(OS.days, OS.status) ~ MEbrown, data = survplotdata), data = survplotdata, risk.table = TRUE, pval = TRUE, break.time.by = 500 ...
written 26 days ago by modarzi80
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Comment: A: Survival analysis with gene expression
... Hi Dr. Blighe, My survplotdata is as below: OS.days OS.status MEbrown TCGA_K1_A3PO 1622 1 -2.33294095 TCGA_IE_A4EI 594 1 0.58743015 TCGA_DX_A6B7 1143 1 -0.54661312 TCGA_HB_A5W3 384 0 -0.5 ...
written 27 days ago by modarzi80
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Comment: C: How to find p-value of the modules in WGCNA?
... Dear Dr. Blighe I construct my co-express network but I don't know how can I calculate module 'scores' for each sample to each module. In other words, I can't manage the below table that you suggested in the last comment: Module1 Module2 ... ModuleX Sample1 0.66 0.43 ... ...
written 29 days ago by modarzi80
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Comment: C: How to find p-value of the modules in WGCNA?
... Dear Dr. Blighe I construct my co-express network but I don't know how can I calculate module 'scores' for each sample to each module. In other words, I can't manage the below table that you suggested in the last comment: Module1 Module2 ... ModuleX Sample1 0.66 0.43 ... 0.33 Sam ...
written 29 days ago by modarzi80
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Comment: C: Survival analysis with gene expression
... Ok, Thanks for your comment. logically, doing multivariate Cox Regression for lots of genes(more than 150 genes) is true? if you agree, how can I run it? can you guide me by tutorial such as the above tutorial? ...
written 5 weeks ago by modarzi80
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Comment: C: Survival analysis with gene expression
... Dear Dr. Blighe I use TPM(Transaction per million) method for normalizing my RNA-Seq data set. base on your perfect tutorial I ran *RegParallel()* for getting survival analysis. I need your comment for 2 below questions: 1- I use 'coxph' as FUNtype for the regression model. is it a suitable functi ...
written 5 weeks ago by modarzi80

Latest awards to modarzi

Student 9 days ago, asked a question with at least 3 up-votes. For Problem for getting P-Value in Module-Trait Relationship in WGCNA
Popular Question 25 days ago, created a question with more than 1,000 views. For how to calculate or extract Circular RNA expression via RNA-seq data
Centurion 29 days ago, created 100 posts.
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Evaluation of HISAT2 Alignment Result
Popular Question 4 months ago, created a question with more than 1,000 views. For how to calculate or extract Circular RNA expression via RNA-seq data
Popular Question 5 months ago, created a question with more than 1,000 views. For Evaluation of HISAT2 Alignment Result
Supporter 13 months ago, voted at least 25 times.

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