PAM50 analysis from RNAseq data
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4.0 years ago
mmeghana ▴ 10

Hello,

I'm analyzing a RNAseq breast cancer data that was sequenced inhouse. I want to classify the samples into their respective subtypes based on PAM50. To do this, I was suggested to use genefu package. I am quite a beginner and I wanted to know the format of required input file and annotation file for genefu package. It would be really helpful if someone could get me through this.

Thank you

PAM50 RNA-Seq • 1.5k views
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4.0 years ago

Hey there,

You should first go through the vignette, genefu: a package for breast cancer gene expression analysis, so that you can then better understand the input format that is required.

Kevin

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Hey Kevin,

Thank you for your response. Will go through the link.

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the genefu updated link is here

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