pathview run problem

Question

[jinxinhao1988]

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:

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.

[seta]

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.

[jinxinhao1988]

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.

[WouterDeCoster]

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

[jinxinhao1988]

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.

Answer 1

[bigmawen]

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