User: rin

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rin20
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Posts by rin

<prev • 24 results • page 1 of 3 • next >
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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 10 days ago by rin20 • updated 10 days ago by RamRS19k
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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 10 days ago by rin20 • updated 10 days ago by RamRS19k
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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 weeks ago by rin20
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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 weeks ago by rin20
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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 10 weeks ago by rin20
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Comment: C: Log2(x + 1) transformation in gene expression not normally distributed.
... @Devon Ryan @b.nota @russhh Really helpful link and answers! Thank you! The reason I want them to be normally distributed is to assess the change between tumor and normal expression by computing a Z-score. Would that be possible / have the same interpretation if they fit a Poisson or NB distribution ...
written 10 weeks ago by rin20
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Comment: C: Log2(x + 1) transformation in gene expression not normally distributed.
... Edited! Sorry about that! :) ...
written 10 weeks ago by rin20
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Log2(x + 1) transformation in gene expression not normally distributed.
... Hi all! I am using raw counts data from TCGA. As I want to compute the Z-score between tumor and normal samples, I have to first ensure that my data are normally distributed. Until now, I downloaded raw counts, normalized them for their GC content using TCGAanalyze_Normalization() function from TCG ...
z-score rna-seq transformation written 10 weeks ago by rin20
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Applying WGCNA in multiple data types
... Hi all As the newbie I am, I would really appreciate your help! I would like to apply a similar approach to WGCNA, but taking into account more than one omics data types, so I cannot use WGCNA itself (I think). I was considering doing the following: 1. Instead of the co-expression measure, I wil ...
wgcna correlation multiomics written 3 months ago by rin20 • updated 10 weeks ago by Kevin Blighe33k
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Comment: C: GISTIC input parameters.
... Thanks for your answer! I was not aware for that option, but I cannot use it as my data are mapped on hg38. TCGA masked copy number data might be an alternative I guess? (They include only somatic variations while germline variations are filtered out) ...
written 3 months ago by rin20

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Supporter 10 weeks ago, voted at least 25 times.

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