User: rina

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rina0
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Posts by rina

<prev • 18 results • page 1 of 2 • next >
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DEP package - Understanding the results table
... Hi all, I am using the DEP package to identify the differentially expressed proteins from my MS results. I have a naive question about the results table. When we get a ratio of -2, for example, for protein A in the contrast Cond1_vs_Cond2. Does that mean that protein A is underexpressed in Cond2 wh ...
proteomics logfc dep written 9 weeks ago by rina0
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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 9 months ago by rina0
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Comment: C: variancePartition - testing for individuals
... 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 9 months ago by rina0
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Oncoplot with own MutSig file
... 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( ...
mutsig maftools written 9 months ago by rina0
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Comment: C: variancePartition - testing for individuals
... 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 9 months ago by rina0
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Comment: C: variancePartition - testing for individuals
... 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 9 months ago by rina0
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variancePartition - testing for individuals
... 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 ...
expression formula variance written 10 months ago by rina0 • updated 10 months ago by mikhael.manurung200
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Comment: C: edgeR. Known cancer genes are not differentially expressed?
... 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 12 months ago by rina0
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edgeR. Known cancer genes are not differentially expressed?
... 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 ...
edger tcga written 12 months ago by rina0 • updated 12 months ago by Aaron Lun25k
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EdgeR between unequal group sizes?
... 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 ...
rnaseq edger differential gene expression written 14 months ago by rina0 • updated 14 months ago by Gordon Smyth39k

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