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Question: differential expression ballgown pData
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gravatar for sophialovechan
15 months ago by
sophialovechan • 10
sophialovechan • 10 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 • 935 views
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modified 15 months ago by Jennifer Hillman Jackson ♦ 25k • written 15 months ago by sophialovechan • 10
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gravatar for Jennifer Hillman Jackson
15 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 15 months ago by Jennifer Hillman Jackson ♦ 25k

Thank you very much.

ADD REPLY • link written 15 months ago by sophialovechan • 10
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