User: Django

Django • 20

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Posts by Django

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Comment: C: About TCGA CNV data preprocessing

... I have downloaded the masked CNV data filtered germline variation as input data and get the average of all probes per gene. If I just want to use CNV data for cluster analysis, is this right? Thank you for your sharing. Now I know the difference between variation and alteration. Thanks again! ...

written 4 days ago by Django • 20

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Comment: C: About TCGA CNV data preprocessing

... Hi, Thanks for your help! I just downloaded the CMV data from TCGA database and mapped genomic regions to gene symbols using the following code: mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") genes <- getBM(attributes=c("hgnc_symbol","chromosome_name","start_posit ...

written 5 days ago by Django • 20

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About TCGA CNV data preprocessing

... Hello all, I am looking at the Level 3 CNV files on TCGA. I have a few questions: I download copy number variance data from TCGA database and mapped genomic regions to gene symbols using this method(https://www.biostars.org/p/311199/#311746). Now i get a matrix that its rows are genes and its colum ...

snp cnv written 5 days ago by Django • 20 • updated 5 days ago by Kevin Blighe ♦ 30k

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About TCGA CNV probes

... Hello all, I am looking at the Level 3 CNV files on TCGA. I have a few questions: I have downloaded the CNV data from TCGA. The details are as follows: GDC_Aliquot Chromosome Start End Num_Probes Segment_Mean Sample 9f3983d5-2f2d-4761-9b4d-4a2ea22ada7b 1 62920 953279 64 -0.2437 TCGA-AR-A0U0-10A- ...

snp cnv written 8 days ago by Django • 20 • updated 8 days ago by Pin.Bioinf • 170

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