User: modarzi

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modarzi10
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Posts by modarzi

<prev • 28 results • page 1 of 3 • next >
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Comment: C: Error via running GDCdownload() in TCGAbiolinks
... Hi, My OS is windows 10. when I run getwd() I see below path: "E:/Biology_base/RNA-seq/GDC-TCGA-SARC/Original_data/SARC RNA-seq by TCGAbiolink Package-971215" so when I run below code: GDCdownload(query) in "SARC RNA-seq by TCGAbiolink Package-971215" folder I see new folder by "GDCdata" ...
written 14 days ago by modarzi10
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Error via running GDCdownload() in TCGAbiolinks
... Hi, I provide below *query*: query <- GDCquery(project = "TCGA-SARC",sample.type = "Primary solid Tumor", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification",workflow.type = "HTSeq - FPKM-UQ"); after that for ...
download tcga tcgabiolinks written 14 days ago by modarzi10 • updated 14 days ago by Tiago Chedraoui Silva170
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Comment: C: WGCNA: What is `soft thresholding`?
... Dear  Lluís Revilla Sancho Thank for your good description. I know that in pickSoftThreshhold function, we can test different power as input by some parameter. for example, for my new analysis, I get below results: Power  SFT.R.sq    slope   truncated.R.sq       mean.k.      median.k.       max.k. ...
written 3 months ago by modarzi10
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Comment: C: problem for Using RNA-seq data-set in WGCNA
... Dear Professor Langfelder Thanks for your comment. Now, I used Ensemble gene_id instead Probes and alternate of Locus Link ID used Gene_Symbol. I have to say that I tried to mapping my Ensemble Gene IDs to Entrez IDs by "biomaRt" package but unfortunately my all gene types didn't have one to one ma ...
written 5 months ago by modarzi10
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Comment: C: Problem for finding "Locus Link ID" from Annotation file
... Dear Dr. W.MacDonald Hello, Thanks for your comment. You are right. WGCNA is not Bioconductor package and my presenting of question  is wrong. Actually my problem relate to converting Ensemble IDs to Entrez IDs. I have Ensemble IDs and also Symbol Genes So based on theses information I would like ...
written 5 months ago by modarzi10
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Error for converting from gene symbol to Entrez IDs
... Hi, For my study, I have to convert gene symbols to Entrez IDs. So, by using "org.Dr.eg.db" package and  my annotation file(annot) I wrote below code: library("org.Dr.eg.db") keytypes(org.Dr.eg.db) k= c("RP11-34P13.7","DDX11L1","RP4-591L5.1" ) kname<- bitr(k, fromType="SYMBOL", toType=("ENTR ...
org.dr.eg.db entrez id written 5 months ago by modarzi10 • updated 5 months ago by James W. MacDonald49k
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Comment: C: problem for Using RNA-seq data-set in WGCNA
... Dear Professor Langfelder Thanks for your comment. As you know, in WGCNA analysis for  Gene Enrichment Analysis and also GO study I need "Locus Link ID". based on below code I have to have "Locus Link ID" but in my annotation file(gencode.v22.genes.csv) I don't have this field: annot = read.csv(f ...
written 5 months ago by modarzi10
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Problem for finding "Locus Link ID" from Annotation file
... Hi, Generally, based on  annotation file(below link) for TCGA data, I don't have  "LocusLinkID" as an attribute for genes. but as you see in below code of WGCNA tutorial, for Interfacing network analysis with other data such as functional annotation and gene ontology I need "LocusLinkID": # Read ...
ensembl tcga wgcna package locuslinkid genecode written 5 months ago by modarzi10 • updated 5 months ago by James W. MacDonald49k
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Comment: C: problem for finding soft thresholding in WGCNA algorithm
... Thanks for your comment.I do apologize for my frequent questions. you said about other metrics addition SFT.R.sq. what metrcis are as your porpuse for using 5 instead 6? and next question:I will use power as 5 for unsigned network. based on my "pickSoftThreshold" result, wich power is suitable for ...
written 5 months ago by modarzi10
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Comment: C: problem for finding soft thresholding in WGCNA algorithm
... Thanks for your comment: for better choosing power, I print the result of "pickSoftThreshold" as below:    Power SFT.R.sq  slope     truncated.R.sq      mean.k. median.k. max.k. 1      1    0.689       12.600          0.608             5770.00  6.14e+03  10700 2      2    0.265       -2.080        ...
written 5 months ago by modarzi10

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