User: rin

gravatar for rin
rin20
Reputation:
20
Status:
New User
Location:
Last seen:
2 days, 21 hours ago
Joined:
3 months, 1 week ago
Email:
e**************@gmail.com

Posts by rin

<prev • 22 results • page 1 of 3 • next >
0
votes
0
answers
63
views
0
answers
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 10 days ago by rin20
1
vote
0
answers
63
views
0
answers
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 11 days ago by rin20
0
votes
1
answer
274
views
1
answers
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 21 days ago by rin20
0
votes
2
answers
169
views
2
answers
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 21 days ago by rin20
0
votes
2
answers
169
views
2
answers
Comment: C: Log2(x + 1) transformation in gene expression not normally distributed.
... Edited! Sorry about that! :) ...
written 21 days ago by rin20
4
votes
2
answers
169
views
2
answers
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 22 days ago by rin20
0
votes
1
answer
110
views
1
answer
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 5 weeks ago by rin20 • updated 23 days ago by Kevin Blighe30k
0
votes
0
answers
137
views
0
answers
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 6 weeks ago by rin20
1
vote
0
answers
137
views
0
answers
GISTIC input parameters.
... Hi everyone I am running GISTIC 2.0 in segmentation data from TCGA and I was wondering whether it is advisable to set the input parameters as default or change the different thresholds. Running the analysis with everything on default and by only changing the confidence level to 0.99, I got many reg ...
gistic snp cnv written 6 weeks ago by rin20 • updated 6 weeks ago by EagleEye5.8k
0
votes
2
answers
335
views
2
answers
Comment: C: Mapping Ensembl IDs to Entrez - Merge data frames
... I was mistakenly putting the Ensembl ID column instead of the whole data frame as an argument to the left join function. It worked just fine now. Thanks for helping! ...
written 11 weeks ago by rin20

Latest awards to rin

Supporter 21 days ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1761 users visited in the last hour