error in R
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9 weeks ago

Can you help me why these errors happen?


$design
  groupCin. groupMet. groupNotreat.
1         0         0             1
2         1         0             0
3         0         1             0
attr(,"assign")
[1] 1 1 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

> cont.matrix <- makeContrasts(CinVsMet = groupCin. - groupMet. ,levels=design)
*Error in eval(ej, envir = levelsenv) : object 'groupCin.' not found*
> cont.matrix
               Contrasts
Levels          CinVsMet
  groupCin.            1
  groupMet.           -1
  groupNotreat.        0

fit.cont <- contrasts.fit(fit, cont.matrix)
 fit.cont <- eBayes(fit.cont)
*Error: evaluation nested too deeply: infinite recursion / options(expressions=)?*
> options(expressions=20000)
> fit.cont <- eBayes(fit.cont)
*Error: node stack overflow*
RNASeq • 704 views
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Please format your code in a proper way and give more details on what you're doing and what you're trying to achieve!

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I've formatted OP's code but given that they have added no context, I doubt we'll be able to help them.

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Please take this forum seriously and learn how to ask good questions, for your benefit, the benefit of others, and for those trying to help you. There is simply no way anyone can answer the question above in the state in which you posted it.

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I searched and googled to find the reasons for the errors in my R file and could not find a solution. one of the members requested me to share more information about my programming,.This helps that the other members who have high skills in R programming and RNA analysis give me some idea or solution. What does it mean "take this forum seriously"?

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Just showing the script is not going to give us all info that is required to help you. Which package is this? What have you already tried to solve the error? Did you read the manual?

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Yes,

I went through this pipeline

https://combine-australia.github.io/RNAseq-R/06-rnaseq-day1.html

But I have 3 samples without replication

groupCin. 
groupMet.
groupNotreat.
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"I tried to follow the recipe for french onion soup, but I have yogurt" is kinda what this sounds like. Instead, tell us exactly which part you're trying to change, what change you're making and the exact error you're running into. "I'm trying to replace XYZ ingredient with yogurt and it tastes really sour" makes things a lot clearer, no?

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My problem is, I can not upload some libraries. So I can not follow of pipeline:For example, I can not add library(org.Hs.eg.db): I have R4.1, how I find higher version Bioconductor?

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installation paths not writeable, unable to update packages

library(org.Hs.eg.db) Error in library(org.Hs.eg.db) : there is no package called ‘org.Hs.eg.db’

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Is this your first time using R? You've made lots of posts with basics R questions. I would suggest you to take a look into some R basics and make some efforts on debugging the errors.

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installation paths not writeable, unable to update packages

The error is all clear... Do you have admin access to your machine?

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Did you read the whole of my questions?

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Yes I did, it still doesn't make complete sense

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