Question: Error with Prunus persica GO Terms in goseq package in R
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gravatar for cr.balladares.m
3.1 years ago by
cr.balladares.m10 wrote:

Hello.

I'm traying to run a GO analysis with the R package "goseq" but I have problems finding the GO Terms mappings for Prunus Persica genes. I understand that goseq needs the name of the gene and the corresponding GO term (ej: GO:0000014 AT3G52115). In the GDR FTP repository there's a "Prunus_persica_v2.0.a1_genes2GO.txt" file, but when running in goseq it throws me this error:

pwf=nullp(diff_express, bias.data=lengths, plot.fit=TRUE) Error in "row.names<-.data.frame"("tmp", value = value) : duplicate 'row.names' are not allowed In addition: Warning message: non-unique values when setting 'row.names': ‘-’, ‘Prupe.1G015800’, ‘Prupe.1G023400’, ‘Prupe.1G036900’, ‘Prupe.1G051600’, ‘Prupe.1G065300’, ‘Prupe.1G073300’, ‘Prupe.1G081800’, ‘Prupe.1G083200’, ‘Prupe.1G088300’, ‘Prupe.1G095400’, ‘Prupe.1G103000’, ‘Prupe.1G108400’, ‘Prupe.1G120600’, ‘Prupe.1G120800’, ‘Prupe.1G124400’, ‘Prupe.1G131400’, ‘Prupe.1G163700’, ‘Prupe.1G166400’, ‘Prupe.1G166700’, ‘Prupe.1G168000’, ‘Prupe.1G174800’, ‘Prupe.1G185400’, ‘Prupe.1G188100’, ‘Prupe.1G189000’, ‘Prupe.1G193700’, ‘Prupe.1G206400’, ‘Prupe.1G217600’, ‘Prupe.1G218900’, ‘Prupe.1G229000’, ‘Prupe.1G234600’, ‘Prupe.1G236400’, ‘Prupe.1G240700’, ‘Prupe.1G243400’, ‘Prupe.1G244900’, ‘Prupe.1G276000’, ‘Prupe.1G280000’, ‘Prupe.1G285700’, ‘Prupe.1G289900’, ‘Prupe.1G314100’, ‘Prupe.1G332600’, ‘Prupe.1G334500’, ‘Prupe.1G342900’, ‘Prupe.1G350900’, � [... truncated]

I load the data by running this command: cat_map=read.table("./Prunus_persica/GO/Prunus_persica_v2.0.a1_genes2GO.txt", head=F, sep="\t")

ADD COMMENTlink modified 3.1 years ago by EagleEye6.3k • written 3.1 years ago by cr.balladares.m10
0
gravatar for EagleEye
3.1 years ago by
EagleEye6.3k
Sweden
EagleEye6.3k wrote:

If you have a gene list and want to find pathways associated with your set of genes, then try GeneSCF V1.1 enrichment tool.

Follow the documentation provided in the tool.

GeneSCF v1.1 enrichment tool now supports all organisms from KEGG.

http://genescf.kandurilab.org/

Example input gene_list format

PRUPE_ppa001641mg

PRUPE_ppa002424mg

PRUPE_ppa002490mg

PRUPE_ppa002592mg

PRUPE_ppa002825mg

PRUPE_ppa002932mg

PRUPE_ppa003086mg

PRUPE_ppa003096mg

PRUPE_ppa003108mg

PRUPE_ppa003316mg

PRUPE_ppa003354mg

PRUPE_ppa003382mg

PRUPE_ppa003458mg

PRUPE_ppa003487mg

PRUPE_ppa003512mg

PRUPE_ppa003635mg

PRUPE_ppa003647mg

PRUPE_ppa003847mg

PRUPE_ppa003869mg

PRUPE_ppa003986mg

PRUPE_ppa003994mg

PRUPE_ppa004007mg

PRUPE_ppa004036mg

PRUPE_ppa004086mg

PRUPE_ppa004145mg

PRUPE_ppa004214mg

PRUPE_ppa004434mg

PRUPE_ppa004441mg

PRUPE_ppa004461mg

PRUPE_ppa004471mg

PRUPE_ppa004610mg

PRUPE_ppa004622mg

ADD COMMENTlink written 3.1 years ago by EagleEye6.3k
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