User: Matina
Matina • 170
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Posts by Matina
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... Hi, by "comparing expression levels between sample groups" you mean differential expression analysis? ...
written 8 months ago by
Matina • 170
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... Hi Atakan,
This is correct - I got an answer from one of the developers of TCGAbiolinks at the [Github account][1] saying that everything that starts with `subtype_` is actually metadata from papers that analyzed the samples suggested to use `days_to_death`. In any case what is strange is that the ...
written 18 months ago by
Matina • 170
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... Thank you very much Igor!
I will have a look at this! ...
written 18 months ago by
Matina • 170
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... Hi Efstathios,
I have a set of genes that I am interested in and I want to see if they are associated with clinical outcomes and molecular subtype patterns. You are right, I got an answer in the GitHub account.
Thanks a lot for your answer!
Matina
...
written 18 months ago by
Matina • 170
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... Hi all,
I have downloaded the TCGA-BRCA RNA-seq data and the associated clinical information using the code below.
CancerProject <- "TCGA-BRCA"
query <- GDCquery(project = CancerProject,
data.category = "Transcriptome Profiling",
dat ...
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Comment:
C: Similar samples in RNAseq
... Have you looked at Pearson correlation between the samples of interest? ...
written 19 months ago by
Matina • 170
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... Hi vinayjrao,
I think the problem is with the `data` matrix; `molecular.subtyping` fuction expects a matrix of samples(rows) x genes(cols). As I can see above your data matrix is genes x samples, right? Try transposing the matrix.
From the genefu vignette for do.mapping: `TRUE if the mapping thro ...
written 19 months ago by
Matina • 170
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... Great! Happy to help! I'll post it as an answer then. ...
written 19 months ago by
Matina • 170
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... Hi vinayjrao,
I think the problem is with the `data` matrix; `molecular.subtyping` fuction expects a matrix of samples(rows) x genes(cols). As I can see above your data matrix is genes x samples, right? Try transposing the matrix. Let me know if it solved your problem!
From the genefu vignette fo ...
written 19 months ago by
Matina • 170
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... Ok, so have you tried using lets say EdgeR or DESeq2 with the raw read counts? If you would prefer to use the normalised data you could use a limma-voom solution. As for GSEA, after you determine differentially expressed genes between the groups of interest you can rank the genes based on some crite ...
written 19 months ago by
Matina • 170
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