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pathview run problem

When I run pathview R package,I use command line like this: pathview_out <- pathview(gene.data = correl_exptable[,1],pathway.id = 00010,species = "cre",out.suffix = "cc849correl",kegg.native = T) and I got this warning:enter image description here

if it is because kegg now is charged for some download, and I am not a pay user.or something else. Have anyone encounter the same situation? And how do you fix it? Thank you.

pathview rna-seq software error
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updated by bigmawen bigmawen • written by jinxinhao1988 jinxinhao1988

No, it is not related to pay, please try with "00010" instead of 00010. If the problem still remains, please tell us your input format, gene identifier.

• 1 views • link
written by seta seta

Thank you very much. I have got a png result file after adding the "". Still it is not a perfect outcome. maybe I should do more adjustments.

• 1 views • link
written by jinxinhao1988 jinxinhao1988

It's good practice to mention your version of R and the packages you are running, by giving the output of sessionInfo()

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written by WouterDeCoster WouterDeCoster

Thank you. My problem has been solved by seta. My R version is R version 3.2.4 Revised (2016-03-16 r70336) and the package I use is Pathview. Thanks all the same.

• 1 views • link
written by jinxinhao1988 jinxinhao1988

1 answer

Here pathway.id should be character (with quote) instead of numeric. The numeric value 00010 in your code got converted to 10 automatically in R, which is not a pathway ID anymore. Therefore you saw the error message above.

Please check pathview function documentation for more details:

?pathview

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written by bigmawen bigmawen

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