User: veronico

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veronico50
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Posts by veronico

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Comment: C: TCGA survival analysis using >100 genes
... Ok, thank you. I'll look into `apply` ...
written 5 days 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 5 days 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 5 days ago by veronico50 • updated 5 days ago by h.mon27k
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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 7 days ago by veronico50
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Comment: C: EPIC array - find probes that are in promoters
... Thank you!!!!!!!!! This is really helpful! ...
written 14 days 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 14 days ago by veronico50
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Comment: C: EPIC array - find probes that are in promoters
... Would you know also how to categorize the probes by which region they are found (body, 5'UTR, intron, etc...)? The manifest has a column that explains this, but it is a bit confusing. For example, one region is explained to be "5'UTR;TSS200;TSS200;Body". ...
written 22 days ago by veronico50
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Comment: C: EPIC array - find probes that are in promoters
... Thank you for your advice! It is really helpful! ...
written 22 days ago by veronico50
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EPIC array - find probes that are in promoters
... Hi everyone, I found some DMPs from a few samples, and have now a list of probes. However, these probes are probably from different parts of the genome and I am only interested in the ones that are found in promoters. I was wondering if anyone had a recommendation on how to do this. I have the coor ...
methylation blog written 22 days ago by veronico50 • updated 17 days ago by Charles Warden7.2k
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Help with EPIC methylation array data analysis - minfi, noob and dmpfinder
... I have EPIC data from 8 samples. Sample sheet: Sorry I am new to posting here, so please forgive my bad formatting: Plate Bead chip # Well Position Well Position Sentrix_ID Array Complete Barcode Sample_Name 1447 1 A01 01A 201172520042 R01C01 201172520042_R01C01 MCF10A N 2d 1447 1 B01 ...
R written 28 days ago by veronico50

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