Find top genes that correlate with my gene of interest using TCGA RNA-Seq data and CCLE data in R.
Hi everyone .
I know some basics i R. I want to use R to find the top genes whose expression correlates with my gene of interest using TCGA RNA-Seq datasets and CCLE datasets to generate a figure depicting the correlation.
I take tcga and ccle data and ı make normalization and filtering.
It looks like this. How can I make table then correlation afterthat.
Can you help me?
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Hamid Ghaedi
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Dila •
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Dila •
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If you are looking for correlation coefficients, then calculating the correlation matrix would be an option:
I get nothing from this code. I want to find top genes that correlate with my gene of interest using TCGA RNA-Seq data and CCLE data in R. This data TCGA brca cancer data. First column is include all genes. I can't select my gene of interest to find correlated genes. What should I do?
The code is not a 'plug and play' one. Why you don't post your effort (code) in R here so more help from more people you would get once they see your efforts. P.S the gene names are in row names and NOT a column.
rownames(df)would return a character vector of gene names.