User: Matina
Matina • 160
- Reputation:
- 160
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- Location:
- United Kingdom/University of Edinburgh
- Last seen:
- 7 months ago
- Joined:
- 5 years, 6 months ago
- Email:
- m******************@gmail.com
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Posts by Matina
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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 9 months ago by
Matina • 160
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... Thank you very much Igor!
I will have a look at this! ...
written 9 months ago by
Matina • 160
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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 9 months ago by
Matina • 160
11
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6 follow
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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 10 months ago by
Matina • 160
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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 10 months ago by
Matina • 160
0
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... Great! Happy to help! I'll post it as an answer then. ...
written 10 months ago by
Matina • 160
1
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1
answer
891
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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 10 months ago by
Matina • 160
0
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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 10 months ago by
Matina • 160
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... So like a kind of feature selection type of analysis? If that is the case you could look for co-expression patterns in genes in specific samples/groups of samples. Another option is to use machine learning methods such as Recursive feature elimination (RFE). For my own analysis I have been using the ...
written 10 months ago by
Matina • 160
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For A: PAM50 subtype classification by genefu
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