PAM50 analysis from RNAseq data

Question

[mmeghana]

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

Answer 1

[Kevin Blighe]

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

[mmeghana]

Hey Kevin,

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

[DareDevil]

the genefu updated link is here