hi,
i am using RobiNA to perform gcrma normalization on my arabidopsis thaliana CEL files. without using my ATH1121501_At_TAIRG.cdf file, the output is with Affymetrix ATH1 Genome Array IDs like 267636_at but i need the output with TAIR locus ID like AT3G34250 but when using my ATH1121501_At_TAIRG.cdf file, i get this error
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unlist, unsplit
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘limma’
The following object is masked from ‘package:BiocGenerics’:
plotMA
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Loading required package: affyio
Adjusting for optical effect....................................................................................................................................................................Done.
Computing affinities[1] "Checking to see if your internet connection works..."
[1] "Environment importcdfcdf was not found in the Bioconductor repository."
[1] "Checking to see if your internet connection works..."
[1] "Environment importcdfprobe was not found in the Bioconductor repository."
Error in get(probepackagename) : object 'importcdfprobe' not found
Calls: gcrma -> bg.adjust.gcrma -> compute.affinities -> get
Execution halted
i installed all of mentioned package. how i can have a gcrma normalized output with
TAIR locus ID like AT3G34250 please???
When providing information to help people diagnose your problem, the more important thing to show is your code! What you have provided is almost everything but the part that would actually be useful. In addition, this isn't really the site you should be consulting. Although RobiNA appears to use Bioconductor tools, it is wrapping those tools in some Java code that seems to be mucking things up. For instance, the AffyBatch apparently has its annotation slot changed to be 'importcdf', which is not the name of any array. Perhaps you need to already install something?
Anyway, if you want to use Bioconductor tools directly, then we are more than happy to help you get going. But if you want to use RobiNA, then you need to ask them what the problem is.
thank you,
excuse me, i have another question, i was going to do vsn normalization on my arrays but i don't know how to write the result as a text file..i did like below
> setwd("E:/Affy data")
> library(affy)
> library(vsn)
> celFiles <- list.celfiles()
> affyraw=ReadAffy(filenames = celFiles)
> affyraw.vsn2=vsn2(affyraw)
vsn2: 506944 x 8 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit.
but hereafter i don't know how to save the normalized file in a txt file because when i wrote like below i got these errors
> write.table(affyraw.vsn2, file = "arrayvsn.txt", dec = ".", sep = "\t", quote = FALSE)
Error in as.data.frame.default(x[[i]], optional = TRUE) :
cannot coerce class "structure("vsn", package = "vsn")" to a data.frame
may you help me please?