Warning about recycled values

[renozao]

Hi,

I am getting this warning when running fgsea on reactome pathways obtained from the package's reactomePathways function, using my top 100 genes:

Warning messages:
1: In `[.data.table`(pvals, , `:=`(leadingEdge, list(leadingEdges))) :
  Supplied 192 items to be assigned to 745 items of column 'leadingEdge' (recycled leaving remainder of 169 items)

The returned value contains many NAs in place of the pathways. Will try to narrow this issue down, but maybe you can check if there is no cbind operation that would lead to this.

[assaron]

Hi,

Could you paste list of genes that you're checking?

On Tue, Aug 23, 2016, 17:44 Renaud Gaujoux notifications@github.com wrote:

Hi,

I am getting this warning when running fgsea on reactome pathways obtained from the package's reactomePathways function, using my top 100 genes:

Warning messages: 1: In [.data.table(pvals, , :=(leadingEdge, list(leadingEdges))) : Supplied 192 items to be assigned to 745 items of column 'leadingEdge' (recycled leaving remainder of 169 items)

The returned value contains many NAs in place of the pathways. Will try to narrow this issue down, but maybe you can check if there is no cbind operation that would lead to this.

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[assaron]

@renozao Unfortunately, I can't replicate this error. Can you, please, provide more information?

[renozao]

Well... I tried and I could not reproduce it either!!! Not sure what was the cause of the error. Maybe I had NA values in my inputs. Problem solved :)

[assaron]

Great it worked out, but I'm still wondering what have happened.