User: modarzi

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modarzi10
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Posts by modarzi

<prev • 14 results • page 1 of 2 • next >
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Question: Problem for getting P-Value in Module-Trait Relationship in WGCNA
... Hi, I Use WGCNA for network analysis. So, one of the WGCNA steps is designing plot of Module-Trait Relationship. In this plot, we can see the relationship between different extracted modules and different Trait variables. Also, in this plot we can see P-Value for each Module-Trait Relationship.So, ...
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problem for finding soft power for constructing network in WGCNA algorithm
... Hi, For constructing network I used WGCNA alghorithm.So,before constructing network, I have to determine SFT index. for that, I ran below code:    sft = pickSoftThreshold(MyData, powerVector = powers, verbose = 5) So I get 10 option as below: Power SFT.R.sq ...
rna-seq wgcna package soft power written 9 weeks ago by modarzi10
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problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
... Hi, I run WGCNA for my study.Now, I want to import my network in Cytoscape for visualization. based on WGCNA tutorial, for that purpose I have to run below code: # select modules modules = c("blue","brown") # Select module probes inModule=is.finite(match(moduleColorsFemale,modules)) ...
wgcna rna-seq topological overlap matrix written 10 weeks ago by modarzi10
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Comment: C: Problem for downloading data from Genomic Data Commons portal via TCGAbiolinks p
... Hi @tiagochst Thanks for your comment. I appreciate if you help me for doing what action for solving my problem. Best Regards, Mohammad ...
written 10 weeks ago by modarzi10
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Problem for downloading data from Genomic Data Commons portal via TCGAbiolinks package
... Hi, I wanted to run below query via GDCquey: query <- GDCquery(project = "TCGA-SARC",sample.type = "Primary solid Tumor", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification",workflow.type = "HTSeq - FPKM-UQ") but I got below error: Downloading: 500 kB <s ...
rna-seq tcgabiolinks written 11 weeks ago by modarzi10
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Problem for Splitting reverse and forward reading in my RNA-seq
... Hi, In downloading SRA files for my study I used browser. So, for Paired End read in my samples, I downloaded just one .fastq file(example link for download).Now, I have to separate reverse and forward reads and my each file should spilte to 2 .fastq file. I appreciate if any body share his/her R ...
rna-seq sra reverse reads forward reads written 11 weeks ago by modarzi10
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Comment: C: Error via running GDCquey from TCGAbiolinks package
... Thanks for your comment. I reinstalled it again and downloading was started based on below message: > GDCdownload(query) Downloading data for project TCGA-SARC GDCdownload will download 259 files. A total of 131.671197 MB Downloading as: Fri_Jun_29_15_08_52_2018.tar.gz   But after downloadin ...
written 11 weeks ago by modarzi10
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Comment: C: Error via running GDCquey from TCGAbiolinks package
... I run this command and got these results: > GenomicDataCommons::status() $`commit` [1] "e9e20d6f97f2bf6dd3b3261e36ead57c56a4c7cc" $data_release [1] "Data Release 12.0 - June 13, 2018" $status [1] "OK" $tag [1] "1.14.1" $version [1] 1 ...
written 11 weeks ago by modarzi10
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Comment: C: Error via running GDCquey from TCGAbiolinks package
... but unfortunately for me give below error again: Error in value[[3L]](cond) : GDC server down, try to use this package later ...
written 11 weeks ago by modarzi10
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Comment: C: Error via running GDCquey from TCGAbiolinks package
... Hi, Thanks for your comment. I tried now but unfortunately I received below message again: Error in value[[3L]](cond) : GDC server down, try to use this package later I don't know what is my problem? my query has problem or package needs some update or GDC server really is done? I appreciate ...
written 11 weeks ago by modarzi10

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