unable to find inherited method inRUVG
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@husainmanagori1998-22771
Last seen 23 months ago
germany

i want to remove unwanted variation from mi RNA raw read count data set,i have two sample one is control and other is main data, i tried to run following example: x1<-RUVg(x = more100,cIdx = migenes,k = 1,drop = 0) x=migenes is main data which has 2234 obs and 90 sample along with gene id cidx = migenes is negative control sample which has 641 obs with 90 sample along with gene id

and got error ::Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘RUVg’ for signature ‘"data.frame", "data.frame", "numeric"’** am i running code in correct way?

ruvseq RUVSeq • 929 views
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@james-w-macdonald-5106
Last seen 12 hours ago
United States

By definition, no. If you only have two samples then there is no unwanted variation to remove! In other words, the unwanted variation that RUV is intended to remove is between-sample variation (where by between-sample we really mean 'between samples from the same group'). Since you only have one sample per group, there is no variation between samples from the same group, hence no variability to remove.

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Oh, wait. If you have 90 samples, why do you say you have two samples? That doesn't make any sense at all. You either have 90 or you have two. You can't have both.

Anyway, the correct course of action for you, when presented with an error that says

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘RUVg’ for signature ‘"data.frame", "data.frame", "numeric"’

Is to actually read the error, which says there is no method for a data.frame, and then go 'huh, wonder what the input should be?', after which you go to the help page for this function to see that it says

Arguments:

    x   Either a genes-by-samples numeric matrix or a SeqExpressionSet object containing the read counts.

Which seems pretty self-explanatory?

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thank you @james .from your answer , i understood that , x= need to provide matrix which has geneId and samples. and for cIdx = only geneid or numeric nubers.

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