User: modarzi

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modarzi50
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Posts by modarzi

<prev • 79 results • page 1 of 8 • next >
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Comment: C: R org.Hs.eg.db matching ensembl gene ids with gene symbol
... Hi, Thanks for your comment. I need your guide. I have "original_id" column and alse "gene_name"(e.g. ENSG00000100601.5 and ALKBH1) and I need their "Entrez ID". could you please guide me how do I get "Entrez ID" by biomaRt or other package from "original_id" ? I appreciate if you share your comme ...
written 4 weeks ago by modarzi50
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Comment: C: Error for converting from gene symbol to Entrez IDs
... Hi, Thanks for your comment. No, my genes symbols belongs for Human. based on your comment If I can't use this package for Human genes symbols, what should I do? which package can give me Entrez IDs from my symbols? I appreciate if you share his/her comment with me. Best Regards, ...
written 4 weeks ago by modarzi50
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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, fromT ...
"org.dr.eg.db" package entrez id written 4 weeks ago by modarzi50
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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 9 weeks ago by modarzi50
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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 9 weeks ago by modarzi50 • updated 9 weeks ago by Kevin Blighe32k
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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 12 weeks ago by modarzi50
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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 12 weeks ago by modarzi50
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(Closed) 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 3 months ago by modarzi50
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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 3 months ago by modarzi50
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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 3 months ago by modarzi50

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