## User: rina

rina0
Reputation:
0
Status:
New User
Last seen:
1 week, 6 days ago
Joined:
9 months, 3 weeks ago
Email:
e**************@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

#### Posts by rina

<prev • 17 results • page 1 of 2 • next >
0
86
views
0
Comment: C: Oncoplot with own MutSig file
... To anyone that might be facing the same problem, I managed to solve this by setting > cms1_sig_genes <- "C:/User/path/to/sig.genes/file" > oncoplot(maf = maf.CMS1, top = 30, mutsig = cms1_sig_genes) ...
written 10 weeks ago by rina0
1
143
views
1
... For form <- ~ (1|tumor_stage) analysis runs as normal But in the case of form <- ~ (1|tumor_stage) + (1|submitter_id) Error: number of levels of each grouping factor must be < number of observations ...
written 11 weeks ago by rina0
0
86
views
0
... Hi all, I am trying to produce an oncoplot using the maftools package. I have performed a MutSig analysis myself and I would like to use the results in the plot. I have loaded the cms1_sig_genes in my R environment, but I get the following error. Any ideas how to solve for this? > oncoplot( ...
written 11 weeks ago by rina0
1
143
views
1
... Exactly. It's one sample per patient. This is what I thought the problem was about too, but I don't know how I can solve for this. ...
written 12 weeks ago by rina0
1
143
views
1
... Hi Mikhael, Thank you for your response. I have defined the submitter_id as a factor, but I keep getting the error Error: number of levels of each grouping factor must be < number of observations. Here is the structure of my data, in case it helps. > glimpse(clin[1:3,]) ...
written 12 weeks ago by rina0
1
143
views
1
... Hi all! I am analyzing the variance sources of TCGA expression data using variancePartition. I want to check among others the effect of individuals in the variance, but when I specify it at the formula, I get the following errors: > form <- ~ submitter_id > varPart <- fitExtra ...
written 3 months ago by rina0 • updated 3 months ago by mikhael.manurung50
1
200
views
1
... Hi Aaron, Thanks for your comment. The patients groups I am analyzing are grouped together according to their molecular subtypes (that themselves are defined based on expression data), so I would assume that this reduces the variability across the samples. Please correct me if I am wrong. As for y ...
written 5 months ago by rina0
1
200
views
1
... Dear experts! I am performing an EdgeR analysis in TCGA samples. I have a subset of the 83 patients I want to check their differential expression in comparison to the 41 samples of normal tissue. Checking for the differential expression of known critical genes (basically almost all the genes taking ...
written 5 months ago by rina0 • updated 5 months ago by Aaron Lun23k
1
215
views
1
... Hi all I am using TCGA data in order to find differentially expressed genes. The cohort I am using has just 41 normal samples, while the tumor subtypes I am working with have measurements ranging from 80 to 140 samples. Is EdgeR (or any other equivalent package) an option or I cannot get significan ...
written 7 months ago by rina0 • updated 7 months ago by Gordon Smyth37k
1
307
views
1
... This didn't seem to work either. I get the same error regarding the start and end index. ...
written 9 months ago by rina0

#### Latest awards to rina

No awards yet. Soon to come :-)

Content
Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.