User: rin

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rin30
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Posts by rin

<prev • 28 results • page 1 of 3 • next >
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Comment: C: Sample-level differential expression for TCGA samples
... Helpful as always! Thanks for your suggestions and help, Kevin. ...
written 6 weeks 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 6 weeks 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 6 weeks 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 6 weeks 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 11 weeks ago by rin30 • updated 11 weeks ago by RamRS20k
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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 11 weeks ago by rin30 • updated 11 weeks ago by RamRS20k
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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 4 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 4 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 4 months ago by rin30
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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 4 months ago by rin30

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