Question: differential expression ballgown pData
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gravatar for sophialovechan
5 days ago by
sophialovechan10 wrote:

Hi everyone, I am using ballgown to do differential gene expression analysis. But I have a question about the pData file. I am not sure what information should be included in phenotype files. I have four datasets, which are two replicates for two samples. Here is the phenotype files I generated. sample1 sample2 sample3 sample4 e_data_ctab e_data_ctab e_data_ctab e_data_ctab e2t.ctab e2t.ctab e2t.ctab e2t.ctab i_data.ctab i_data.ctab i_data.ctab i_data.cta i2t.ctab i2t.ctab i2t.ctab i2t.ctab t_data.ctab t_data.ctab t_data.ctab t_data.ctab

I also used codes below: pDATA(bg)=data.frame(id=sampleNames(bg),group=rep(c(0,1),each=2)) But I am still getting error when I ruined stattest Error in stattest(bg_2, feature = "transcript", meas = "FPKM", covariate = "group") : to do statistical tests, either gown must contain pData or you must specify models. I am new to R language so I don't know how to troubleshoot this problem. Can someone help me out? I really appreciate your help. Thank you.

rna-seq • 36 views
ADD COMMENTlink modified 5 days ago by Jennifer Hillman Jackson22k • written 5 days ago by sophialovechan10
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gravatar for Jennifer Hillman Jackson
5 days ago by
United States
Jennifer Hillman Jackson22k wrote:

Hello,

This site is focused on helping with data analysis within Galaxy, but we can offer some advice.

For help with the line-command usage of this tool, please see the publication. In short, you will want to adjust your analysis to resolve this usage error message "either gown must contain pData or you must specify models". Sample data is available for download, including a sample of the pData input. Use the example with the sample data to help work out the correct usage, then use the same protocol with your own data.: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5032908/

This prior Q&A has some other related help (in the context of Galaxy): https://biostar.usegalaxy.org/p/23253/

Thanks, Jen, Galaxy team

ADD COMMENTlink written 5 days ago by Jennifer Hillman Jackson22k

Thank you very much.

ADD REPLYlink written 5 days ago by sophialovechan10
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