Question: Need help about mRNA-Seq result
0
gravatar for Halcyon Murphy
11 days ago by
Halcyon Murphy0 wrote:

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.

sequencing rna-seq sequence R • 247 views
ADD COMMENTlink modified 11 days ago by dr_bantz50 • written 11 days ago by Halcyon Murphy0
1

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.

ADD REPLYlink written 11 days ago by WouterDeCoster20k

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.

ADD REPLYlink written 8 days ago by Halcyon Murphy0
1
gravatar for dr_bantz
11 days ago by
dr_bantz50
dr_bantz50 wrote:

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

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

ADD COMMENTlink written 11 days ago by dr_bantz50

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

ADD REPLYlink written 11 days ago by Halcyon Murphy0
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