Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
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@4fc7b6eb
Last seen 5 days ago
United States

Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("simpleaffy")

library("simpleaffy")

Error in library("simpleaffy") :There is no package named 'simpleaffy'


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
simpleaffy • 123 views
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@james-w-macdonald-5106
Last seen 5 minutes ago
United States

You neglected to show any of the intervening output. Which includes this:

Warning message:
In .inet_warning(msg) :
  package 'simpleaffy' is not available for Bioconductor version '3.14'

And if you go to the release announcement for Bioc 3.13, and go waay to the bottom under 'Deprecated and Defunct Packages' you can see that simpleaffy got removed.

Sixty Five software packages were removed from this release (after being deprecated in Bioc 3.12): adaptest, ArrayTV, BioSeqClass, CHARGE, chimera, CNVtools, CorMut, DESeq, explorase, flowFit, flowSpy, flowType, focalCall, FourCSeq, FunciSNP, GeneticsDesign, GenRank, GGBase, GGtools, GOFunction, gQTLBase, gQTLstats, hicrep, ImpulseDE, ImpulseDE2, joda, JunctionSeq, LINC, Logolas, mcaGUI, metaArray, metaseqR, methVisual, methyvim, Mirsynergy, MmPalateMiRNA, MOFA, MotIV, NarrowPeaks, netbenchmark, netReg, OGSA, OmicsMarkeR, pathprint, PathwaySplice, PGA, PGSEA, plrs, prada, Prize, Rariant, reb, Roleswitch, rTANDEM, sapFinder, scsR, shinyTANDEM, sigaR, signet, simpleaffy, spotSegmentation, Starr, SVAPLSseq, TxRegInfra, xps

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Thank you very much for your answer. I'm a green hand. I read this code in a book. I would like to know if there is a substitute for these deleted R packets, or can you tell me the available R packets for analyzing the data of gene chip?

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You should use oligo instead. simpleaffy was meant to work with the affy package, which itself has been superceded by oligo. If you want a good primer, you could read the End to End workflow.

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Thank you very much for your answer, your answer is excellent 👍🏻.

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