User: Matina

gravatar for Matina
Matina150
Reputation:
150
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Location:
United Kingdom/University of Edinburgh
Last seen:
3 months, 2 weeks ago
Joined:
5 years, 2 months ago
Email:
m******************@gmail.com

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Posts by Matina

<prev • 38 results • page 1 of 4 • next >
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Comment: C: TCGAbiolinks TCGA-BRCA RNA-seq clinical data
... 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 6 months ago by Matina150
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Comment: C: TCGAbiolinks TCGA-BRCA RNA-seq clinical data
... Thank you very much Igor! I will have a look at this! ...
written 6 months ago by Matina150
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Comment: C: TCGAbiolinks TCGA-BRCA RNA-seq clinical data
... 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 6 months ago by Matina150
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TCGAbiolinks TCGA-BRCA RNA-seq clinical data
... 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 ...
tcgabiolinks tcga brca rna-seq written 6 months ago by Matina150 • updated 6 months ago by igor7.1k
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Comment: C: Similar samples in RNAseq
... Have you looked at Pearson correlation between the samples of interest? ...
written 7 months ago by Matina150
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Answer: A: PAM50 subtype classification by genefu
... 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 7 months ago by Matina150
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Comment: C: PAM50 subtype classification by genefu
... Great! Happy to help! I'll post it as an answer then. ...
written 7 months ago by Matina150
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Comment: C: PAM50 subtype classification by genefu
... 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 7 months ago by Matina150
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Comment: C: Differential Expression from Quantile-Norm Data
... 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 7 months ago by Matina150
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Comment: C: Deep exploration of an expression atlas
... 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 7 months ago by Matina150

Latest awards to Matina

Supporter 6 months ago, voted at least 25 times.
Scholar 7 months ago, created an answer that has been accepted. For A: PAM50 subtype classification by genefu
Popular Question 14 months ago, created a question with more than 1,000 views. For Ballgown plotTranscripts function
Popular Question 14 months ago, created a question with more than 1,000 views. For Uninstall samtools 1.1 version
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Uninstall samtools 1.1 version
Popular Question 2.7 years ago, created a question with more than 1,000 views. For EdgeR analysis with 3 conditions
Student 2.8 years ago, asked a question with at least 3 up-votes. For EdgeR-GLMs correcting for batch effects
Popular Question 4.0 years ago, created a question with more than 1,000 views. For EdgeR-GLMs correcting for batch effects

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