User: modarzi

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modarzi20
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Posts by modarzi

<prev • 76 results • page 1 of 8 • next >
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Comment: C: problem with facing strange gene name in TCGA data
... Dear Dr. Blighe Hello, Thanks for your comment. Now, what should I do with these genes? can I use them in my analysis or have I to delete them? I appreciate if you share your comment with me. Best Regards, Moha ...
written 5 days ago by modarzi20
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problem with facing strange gene name in TCGA data
... Hi, After Batch corection through TCGA batch effect ewbsite, I downloaded corrected RNA-seq data. when I look at this data, the ID of first few genes are strange. does anybody knows why? gene ?|100130426 ?|100133144 ?|100134869 ?|10357 ?|10431 ?|136542 ?|155060 ...
tcga rna-seq batch effect correction written 11 days ago by modarzi20 • updated 11 days ago by Kevin Blighe28k
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Comment: C: Problem for finding "Locus Link ID" from Annotation file
... Thanks for your comment. You mean, can I use 'gene_id' instead of "Locus Link ID"? ...
written 4 weeks ago by modarzi20
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Comment: C: Problem for finding "Locus Link ID" from Annotation file
... Thanks for your comment. Let me explain more about your solution. I have explained more for my problem by editing my post. I appreciate if you share your comment with me. Best Regards, Mohammad ...
written 4 weeks ago by modarzi20
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Problem for finding "Locus Link ID" from Annotation file
... Hi, I am studing on TCGA RNA-seq. So, I downloaded annotation file via .gtf format that name and version is gencode.v22.genes.gtf . colnames(gencode.v22.genes) "seqname", "source", "feature", "start", "end", "score", "strand", "frame", "gene_id", "gene_name", "gene_status", "gene_type ...
locus link id annotation R wgcna written 4 weeks ago by modarzi20
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Comment: C: Problem for getting P-Value in Module-Trait Relationship in WGCNA
... Dear Dr. Blighe Hi, Thanks for your comments.my code is in below: ###########Relating modules to physiological traits############## # Choose a module assignment moduleColorsSTLMS=moduleColorsAutomatic # Define numbers of genes and samples nGenes = ncol(datExprSTLMS) nSampl ...
written 5 weeks ago by modarzi20
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Comment: C: Problem for getting P-Value in Module-Trait Relationship in WGCNA
... Hi, Thanks for your comment. I need to attached my module-trait relationship plot for showing problem. could you please guide me how can I upload my .pdf file via this post? Description My Problem: I have to work on 53 cancer samples from one of the TCGA Cancer dataset. I used WGCNA for constructi ...
written 5 weeks ago by modarzi20
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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, ...
p-value wgcna network analysis written 5 weeks ago by modarzi20
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Comment: C: problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
... Dear Dr. Blighe Thanks for your comment. based on your guide I have decreased my data dimension from 56000 to 27000. but in 56000 dimension, I had 95 modules and now I have 141 modules. is this situation normal? I appreciate if you share your comment with me. Best Regards, Mohammad ...
written 10 weeks ago by modarzi20
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Comment: C: problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
... Dear Dr. Blighe Thanks for your comment. based on your good recommendation cutoff, MyData has decreased to 27251 genes. So, could you please give me reference for below formula: min + ((max-min) / 2) Best Regards, Mohammad ...
written 10 weeks ago by modarzi20

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