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MaloofLab / Nozue2018_SAStranscriptome_scripts

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goseq permutation method #1

Open knozue opened 6 years ago

knozue commented 6 years ago

@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 commented 6 years ago

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

On Thu, Oct 18, 2018 at 11:32 AM knozue notifications@github.com 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 https://github.com/MaloofLab/Nozue2018_SAStranscriptome_scripts/issues/1, or mute the thread https://github.com/notifications/unsubscribe-auth/ABgfmHSOJOxAQgFOJbnhnkIqr3QQOZy0ks5umMklgaJpZM4XuYQO .

knozue commented 6 years ago

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

jnmaloof commented 6 years ago

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

On Thu, Oct 18, 2018 at 1:37 PM knozue notifications@github.com 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 https://github.com/MaloofLab/Nozue2018_SAStranscriptome_scripts/issues/1#issuecomment-431151552, or mute the thread https://github.com/notifications/unsubscribe-auth/ABgfmNQe3CkepNWwJ9GzCY2-955QWM7aks5umOZ9gaJpZM4XuYQO .