User: rin

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rin30
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Posts by rin

<prev • 29 results • page 1 of 3 • next >
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Too many genes in specific chromosomal regions - GISTIC results
... Hi all I have performed a GISTIC2.0 analysis in my samples, but after analyzing the results I found something that seemed a little off. In the results, there are some regions that are annotated to contain thousands of genes, e.g. 17q21.31 has 1018 genes according with the results. In the meanwhile, ...
gistic cnv written 3 months ago by rin30 • updated 3 months ago by Kevin Blighe43k
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Comment: C: Sample-level differential expression for TCGA samples
... Helpful as always! Thanks for your suggestions and help, Kevin. ...
written 5 months ago by rin30
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Comment: C: Sample-level differential expression for TCGA samples
... Sorry I should have made it more clear :) I don't want different expression between groups (tumor Vs normal) in general, but differential expression of genes in every patient (tumor Vs normal for patient A, patient B and so on). The reason is that after doing the differential expression analysis in ...
written 5 months ago by rin30
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Comment: C: Sample-level differential expression for TCGA samples
... I have performed already a Tumor Vs. Normal DE with EdgeR, but I want to visualize the potential expression differences in sample level in a network I have built. Edit: I am aware that cBioPortal does not have tumor vs. normal analysis when it comes to expression. ...
written 5 months ago by rin30
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Sample-level differential expression for TCGA samples
... Hi all! Is anyone aware of available **sample-level** differential expression from TCGA? I am trying cBioPortal, but for a reason the patient IDs I am using are not recognised. As far as I saw, Firehose does not provide DE data. Thanks in advance. R. ...
tcga de rna-seq deg written 5 months ago by rin30
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Comment: A: Two dimentional mutation lanscape
... Haha I agree, it's not the most good looking one, but it was the only example I found in google. I saw this one from Alberts' Molecular Biology of the Cell book. I attached the figure I am referring to. In general, I am more interested in this mountains-and-hills visualization of the frequency of ...
written 6 months ago by rin30 • updated 6 months ago by RamRS22k
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Two dimentional mutation lanscape
... Is anyone aware of a way to produce a plot similar to this? Thank you in advance! ...
visualization mutations plot written 6 months ago by rin30 • updated 6 months ago by RamRS22k
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Comment: C: GISTIC results. Too many deleted genes?
... Hi Kevin! I am using Masked segmented data from TCGA. And no this is the only tool I have used, so far. ...
written 8 months ago by rin30
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GISTIC results. Too many deleted genes?
... Hi all I am kind of sceptical about some results I got from GISTIC 2.0. Using the following parameters I got a huge number of deleted genes while just a few amplified. More specifically, 587 amplified vs. 3461 deleted. Input parameters used: Amplification Threshold = 0.1 Deletion Threshold = 0. ...
gistic cnv snp written 8 months ago by rin30
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Comment: C: TCGA - Correlation between gene expression and CNV
... Hi Kevin! Coming back to this (almost ancient now) post for a follow-up question! I used indeed DESeq2 with a design of ~tumor + normal. One think I am quite unsure about is whether I should compute the Z-score, as (expression in my samples - mean expression in normal samples) / st. dev of expres ...
written 8 months ago by rin30

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Supporter 8 months ago, voted at least 25 times.

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