User: berry
berry • 20
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Posts by berry
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... Thank you very much, I appreciate it. ...
written 8 weeks ago by
berry • 20
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... 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
berry • 20
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... 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 ...
written 8 weeks ago by
berry • 20
• updated
8 weeks ago by
bruce.moran • 830
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... 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
berry • 20
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... 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 ...
written 8 months ago by
berry • 20
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... 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
berry • 20
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... 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
berry • 20
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... 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
berry • 20
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... Hi,
I have TCGA segment files and I want to analyse the number of breakpoints. Does anyone know how to calculate it?
Thanks! ...
written 9 months ago by
berry • 20
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... 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 ...
written 10 months ago by
berry • 20
• updated
10 months ago by
Kevin Blighe ♦ 63k
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