Dear users,
I am trying to do a micro-array analysis using CEL files for S. aures using R.
- I have used the following libraries:
source("https://bioconductor.org/biocLite.R") library("affy") library("limma") library("genefilter")
- Then I loaded the pd.s.aureus data set using the above and included it using the
library("pd.s.aureus")
- Then using the RMA method I imported the data to eset variable. After that I tried to do a non-specific filtering using nsFilter
esetF <- nsFilter(eset, remove.dupEntrez = FALSE, var.cutoff = 0.5)
Once I do that it gives me the error
Error: getAnnMap: package saureus not available
But I have loaded the "pd.s.aureus" library as there is no annotation data set in the name of saureus. (https://bioconductor.org/packages/3.7/data/annotation/)
Is there anything I am missing here ? Is there a way around this?
Thank you very much and any suggestion is much appreciated
Neranjan
Please don't use the Add your answer box unless you are actually adding an answer.
There is a workflow that covers the basics, and then there is the limma User's Guide, which is a comprehensive guide for fitting a model and making comparisons.
The workflow at F1000 may also be a good place to start.