User: berry

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berry20
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New User
Location:
Belgium
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1 month, 3 weeks ago
Joined:
1 year, 10 months ago
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Posts by berry

<prev • 14 results • page 1 of 2 • next >
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Comment: C: TCGAbiolinks problem downloading ASCAT2 data
... Thank you very much, I appreciate it. ...
written 8 weeks ago by berry20
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Comment: C: TCGAbiolinks problem downloading ASCAT2 data
... Thank you for your reply. My version is 2.17.1 and that doesn't accept sample.type = "Primary solid Tumor". It works with "Primary Tumor". With your code, I'm only able to download "hg19.seg" file. However, I want to download a different type of segment data that is processed with ASCAT2 and fil ...
written 8 weeks ago by berry20
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TCGAbiolinks problem downloading ASCAT2 data
... Hi, I want to download TCGA copy number segment data that is created by ASCAT2 using TCGAbiolinks but I can't specify this data type. Is there a way to do that? I am used to downloading with GDCquery but this time I fail. The files I want to download end in this format "allelic_specific.seg" but ...
tcgabiolinks tcga written 8 weeks ago by berry20 • updated 8 weeks ago by bruce.moran830
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Answer: A: Circle-Map: Sensitive detection of circular DNA at single-nucleotide resolution
... Dear IP, Do you think Circle-Map can also work for shallow-seq (0.1X)? In the paper, I see you also test for low coverage; however, it was 7.5X, which is still higher than my data. Thanks! ...
written 6 months ago by berry20
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Cox regression- testing for effects
... Hi all, I performed hierarchical clustering on my expression data, and I have 3 clusters. I also categorized available treatment types into three groups. Now I want to analyze whether one of my clusters benefit significantly from one of the three treatment types in the presence of gender, age, KPS ...
survival analysis written 8 months ago by berry20
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Comment: C: How to analyse number of breakpoints -TCGA data
... Hi Kevin, what I want to do is to count the number of genome breaks occurring across the genome, in each sample. The breaks where the copy number changes (amplified/deleted). I want to see if there is a difference or a trend in breakpoint counts within the samples I grouped together (ie. which sampl ...
written 9 months ago by berry20
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Comment: C: How to analyse number of breakpoints -TCGA data
... Hi Kevin, You are right. I downloaded the segment files using TCGAbiolinks. And the files look like this : Sample Chromosome Start End Num_Probes Segment_Mean GLAZY_p_TCGA_B20_SNP_N_GenomeWideSNP_6_H03_517846 1 3218610 8355467 3166 -0.0355 GLAZY_p_TCGA_B20_SNP_N_GenomeWideSNP_6_H03_517846 1 8372 ...
written 9 months ago by berry20
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Comment: C: How to do subtype assignment for expression data
... Thanks Kevin! Just to note here for the people who work on GBM, I found this portal to assign expression data to 3 GBM subtypes (Wang et al 2017): http://gliovis.bioinfo.cnio.es/ ...
written 9 months ago by berry20
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How to analyse number of breakpoints -TCGA data
... Hi, I have TCGA segment files and I want to analyse the number of breakpoints. Does anyone know how to calculate it? Thanks! ...
tcga breakpoints written 9 months ago by berry20
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How to do subtype assignment for expression data
... Hi, I'm working with RNA-seq data of GBM (Glioblastoma) samples (tumor only). I want to see which subtype my samples are belong to, based on a previous study which divides GBM into 3 subtypes. Each of these subtypes has 50 signature gene list. What would be the best way of assigning my samples t ...
gbm subtype rna-seq written 10 months ago by berry20 • updated 10 months ago by Kevin Blighe63k

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Supporter 11 months ago, voted at least 25 times.

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