goseq permutation method

[knozue]

@jnmaloof
Please find an example of goseq permutation method in function_RNAseq_time_courss.R under SAS_muts_time_course_RNAseq_finalfilal directory.

line: 875 within GOseq.overlapTable functions

GO.pval <- goseq(pwf,gene2cat=temp,use_genes_without_cat=TRUE,method="Sampling",repcnt=permutation) # format became different in new goseq version (021111)

[jnmaloof]

I think you have the version number wrong; in Bioconductor the version number is 1.32.0 https://bioconductor.org/packages/release/bioc/html/goseq.html Julin Maloof Professor Department of Plant Biology 1 Shields Ave University of California, Davis Davis, CA 95616 (530) 752 8077

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On Thu, Oct 18, 2018 at 11:32 AM knozue ***@***.***> wrote: @jnmaloof <https://github.com/jnmaloof> Please find an example of goseq permutation method in function_RNAseq_time_courss.R under SAS_muts_time_course_RNAseq_finalfilal directory. line: 875 within GOseq.overlapTable functions GO.pval <- goseq(pwf,gene2cat=temp,use_genes_without_cat=TRUE,method="Sampling",repcnt=permutation) # format became different in new goseq version (021111) — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABgfmHSOJOxAQgFOJbnhnkIqr3QQOZy0ks5umMklgaJpZM4XuYQO> .

[knozue]

@jnmaloof Can you tell me where I mentioned the Bioconductor version number?

[jnmaloof]

in the code line that you pasted in your first message. " # format became different in new goseq version (021111)" Julin Maloof Professor Department of Plant Biology 1 Shields Ave University of California, Davis Davis, CA 95616 (530) 752 8077

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On Thu, Oct 18, 2018 at 1:37 PM knozue ***@***.***> wrote: @jnmaloof <https://github.com/jnmaloof> Can you tell me where I mentioned the Bioconductor version number? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABgfmNQe3CkepNWwJ9GzCY2-955QWM7aks5umOZ9gaJpZM4XuYQO> .