Question: PAM50 analysis from RNAseq data
0
gravatar for mmeghana
6 weeks ago by
mmeghana10
mmeghana10 wrote:

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.

rna-seq tool pam50 • 88 views
ADD COMMENTlink modified 6 weeks ago by Kevin Blighe63k • written 6 weeks ago by mmeghana10
0
gravatar for Kevin Blighe
6 weeks ago by
Kevin Blighe63k
Kevin Blighe63k wrote:

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

ADD COMMENTlink modified 5 weeks ago • written 6 weeks ago by Kevin Blighe63k
1

Hey Kevin,

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

ADD REPLYlink written 6 weeks ago by mmeghana10
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