User: veronico

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veronico50
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Posts by veronico

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Cox regression survival analysis - using a panel of genes with TCGA
... the panel of genes came from some analysis from my lab. I included only 4 genes just to simplify it. I get the following graph: https://flic.kr/p/2hvMBui ...
written 7 weeks ago by veronico50
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Comment: C: Cox regression survival analysis - using a panel of genes with TCGA
... Sorry, needed to put the rest of the code in another comment 'cuz I reached the max of characters. # and days last follow up here we take the most recent which is the max number ind_keep <- grep('days_to_last_followup',colnames(clinical)) fl <- as.matrix(clinical[,ind_kee ...
written 7 weeks ago by veronico50
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Comment: C: Cox regression survival analysis - using a panel of genes with TCGA
... Hi Kevin, Thank you so much for answering! I will include my whole code. Basically, I got mRNA-seq data from TCGA (Fire Browser). I followed the instructions from this link (https://www.biostars.org/p/153013/). However, this looks at single genes at a time. So, thankfully the survival package incl ...
written 7 weeks ago by veronico50
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Cox regression survival analysis - using a panel of genes with TCGA
... I am using the survival package in R and have a panel of genes that I want to use to determine if these group of genes affect survival. I towards the end and want to produce the graph, but I keep getting one line graph with what appears confidence lines flanking it. Has anyone used it for a panel ...
tcga panel survival written 7 weeks ago by veronico50 • updated 7 weeks ago by Kevin Blighe52k
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Comment: C: TCGA survival analysis using >100 genes
... Ok, thank you. I'll look into `apply` ...
written 3 months ago by veronico50
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Comment: C: TCGA survival analysis using >100 genes
... for each gene? My apologies I am not following. Would this work if I have a panel of a >100 genes that I want to investigate together? ...
written 3 months ago by veronico50
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TCGA survival analysis using >100 genes
... Hi everyone, I hope everyone is doing well! I was wondering if anyone knew how to do survival analysis by using a panel of >100 genes? I have a list of genes I am interested in (>100 genes) and I want to find these list of genes that are down regulated from RNA seq data from TCGA (preferably ...
many tcga rna-seq survival written 3 months ago by veronico50 • updated 3 months ago by h.mon28k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... Hi TriS, Thank you so much for this tutorial! It is extremely helpful and insightful! My apologies for the potential naive question I will be asking but for the KIRK data, I did the following code and get the following results: > # check how many altered samples we have > table(even ...
written 3 months ago by veronico50
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Comment: C: EPIC array - find probes that are in promoters
... Thank you!!!!!!!!! This is really helpful! ...
written 4 months ago by veronico50
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Comment: C: EPIC array - find probes that are in promoters
... yes, I am using "IlluminaHumanMethylationEPICanno.ilm10b4.hg19" ...
written 4 months ago by veronico50

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