I got error when visualizing my PCA
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m610110001 • 0
@f4448112
Last seen 12 months ago
Taiwan

Hello Guys,

I am using R to visualize my PCA. But I got error messages in here. Anybody know how to solve it?


 >pca.gseUCEC <- PCA(train_dataUCEC,graph = FALSE)
> 
> fviz_pca_ind(pca.gseUCEC, geom = "point", col.ind = sedfUCEC[["secondary_gleason_grade"]])
Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : 
  replacement has length zero
In addition: Warning message:
In rep(yes, length.out = len) : 'x' is NULL so the result will be NULL
> 
> table(sedfUCEC[["secondary_gleason_grade"]])
< table of extent 0 >

sessionInfo( )

Please help to fix the issue, I am new in R and just follow others' code.

Thank you

PCAtools pcaExplorer pcaMethods • 1.1k views
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@federico-marini-6465
Last seen 3 days ago
Germany

Hi m610110001,

With only this snippet of code it is hard to help you on this (i.e. if I cannot reproduce it, I cannot really know what goes on).

Still, a couple of observations:

  • this seems related to the factoextra package (not on Bioc)
  • the message seems quite clear: you have no elements in sedfUCEC[["secondary_gleason_grade"]], as the table command reports

Please do invest more time in "just follow others' code". I know it takes an extra effort, but to the bare minimum, you can help us helping you. This would include

  • making something like a reproducible example
  • grasping what the parameter of a function would expect, what errors are commonly thrown
  • printing out (also for yourself) the output of the commands you enter - it has a lot of value to see right away what formats your data is stored as

... and more, actually, but I don't want to scare you off from asking a question.
What I am saying: it is (much) easier for others to help you solve issues, and in many cases (been there a lot of times) by making it reproducible for yourself, you often find out what went wrong, and with some luck (and experience) you can solve the problem already.

Cheers,
Federico

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Thank you for your answer

I foudn the problem was because I used vector function unlist in r and it got null value

train_dataUCEC <- unlist(t(expr_filteredUCEC))
train_dataUCEC <- log2(train_dataUCEC+0.5)

I am using TCGA dataset for UCEC and OV disease.

How do I send my full script? I also adopt this code from youtube adjusting to my dataset.

Thank you

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There's no need to send me the full script, especially if it worked after fixing the values (passed correctly now, no error seems to be thrown?)

For the next steps: depends on what you plan to do, but my advice would be to follow some established workflows to see how these things are done inside these.
As an example: you might want to check out the fantastic TCGAbiolinks package.

Federico

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