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Need help about mRNA-Seq result

Greetings, everyone.

I am just new to this field and looking for help since the lab majors in medicinal chemistry.

We got mRNA-Seq data of our cells from other lab. The data we have only gives FPKM associated with gene names and subjects. The PI wants me to find out the biomarkers among these cells from mRNA data.

According to the knowledge and references I have, packages from bioconductor are mostly used for this kind of analysis. However, the ones often used like GOSeq, edgeR, DESeq2 require raw data, such as count number from reading. Is there any suggestion what I should use or how I should do?

Thanks for attentions and help.

PS: I cannot get access to the count per million (CPM) or other data. The table with FPKM is all I have.

rna-seq rna-seq sequencing sequence r
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updated by dr_bantz dr_bantz • written by Halcyon Murphy • Halcyon Murphy

We got mRNA-Seq data of our cells from other lab. The data we have only gives FPKM associated with gene names and subjects.

The best you can do is get access to the raw data. Ask the other lab, or have your PI ask them. Having only FPKMs is a severe limitation.

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written by WouterDeCoster WouterDeCoster

Thank you very much. However, I have talked with PI twice and he refused to provide raw data as he considered FPKM was enough. I assume I will be fired if I insist futher since contact of my technician is temporary. I will try to analyze based on FPKM.

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written by Halcyon Murphy • Halcyon Murphy

1 answer

cummeRbund (part of the Tuxedo suite) accepts FPKM input.

http://compbio.mit.edu/cummeRbund/

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written by dr_bantz dr_bantz

Thank you very much! I will learn details about this package.

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written by Halcyon Murphy • Halcyon Murphy

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