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thelovelab / fishpond

Differential expression and allelic analysis, nonparametric statistics
https://thelovelab.github.io/fishpond
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Unused argument (diffAI = TRUE) #37

Closed zhangjy859 closed 9 months ago

zhangjy859 commented 9 months ago

Hi,

I am trying to create a stimulation data following the guide, but I got a error:

library(fishpond)
set.seed(1)
y <- makeSimSwishData(diffAI=TRUE, n=12)
colData(y)

Error in makeSimSwishData(diffAI = TRUE, n = 12) : 
  unused argument (diffAI = TRUE)

I think it's because the version of fishpond seems too old (2.2.0), but this seems to be the latest version in BiocManager on the Windows platform?

Regrads.

Zhang

mikelove commented 9 months ago

Check the man page from R. If you don’t see the argument it indicates you may have an older version.

mikelove commented 9 months ago

Sorry, didn’t see your update.

The version of Bioc package delivered depends on your version of R.

zhangjy859 commented 9 months ago

Hi @mikelove,

Thank you for your prompt reply. My R version is 4.2.1, which doesn't seem to be an outdated version. Is it possible to add support for this R version in the new version?

I successfully created example data in other versions of R. Can I confirm with you about the pair parameter in swish? I am not a method or statistical expert. Based on my understanding of your well written paper, code and examples (my understanding may not be correct), for allelic different analysis, the pair here actually refers to the pairing of two alleles (a1 and a2), not the pairing of samples under two conditions (for example, sample A before and after receiving a certain treatment).

mikelove commented 9 months ago

It’s not possible to change the Bioc installation script. But you can see how to get the latest version here:

https://www.bioconductor.org/install/

yes, we use pair in the AI examples to indicate pairing of the two alleles within a donor.

zhangjy859 commented 9 months ago

Hi @mikelove

Thank you so much for your prompt response to my question! I truly appreciate your efficiency and professionalism.

I will close this issue, once again, thank you for your dedication and support!