Hi friends, I need your help please. I tried to adopt a tutorial in human (GSE27447) to my case in citrus sinensis, I searched a lot in google but I could not find fit equal to some parts and when I did these steps by removing parts I had doubts about, the result was a rma.txt which could not be read in some case (with ????) I do not know what I should type instead of... my query is GSE67376 (citrus sinensis)

source("http://bioconductor.org/biocLite.R")

biocLite("GEOquery")
biocLite("affy")
biocLite("gcrma")
biocLite("hugene10stv1cdf") # changed to biocLite("citruscdf")
biocLite("hugene10stv1probe") # changed to biocLite("citrusprobe")
biocLite("hugene10stprobeset.db") ????????????
biocLite("hugene10sttranscriptcluster.db") ???????

library(GEOquery)
library(affy)
library(gcrma)
library(hugene10stv1cdf) # changed to library("citruscdf")
library(hugene10stv1probe) # changed to library("citrusprobe")
library(hugene10stprobeset.db) ?????????
library(hugene10sttranscriptcluster.db) ?????

setwd("C:/Users/Man/Desktop/New folder (3)")

getGEOSuppFiles("GSE27447")

setwd("C:/Users/Man/Desktop/New folder (3)/GSE27447")

untar("GSE27447_RAW.tar", exdir="data")

cels = list.files("data/", pattern = "CEL")
sapply(paste("data", cels, sep="/"), gunzip)
cels = list.files("data/", pattern = "CEL")

setwd("C:/Users/Man/Desktop/New folder (3)/data")
raw.data=ReadAffy(verbose=TRUE, filenames=cels, cdfname="hugene10stv1") ??????

data.rma.norm=rma(raw.data)
rma=exprs(data.rma.norm)
rma=format(rma, digits=5)

ls("package:hugene10stprobeset.db") #Annotations at the exon probeset level ?????????
ls("package:hugene10sttranscriptcluster.db") ??????????????

probes=row.names(rma)
Symbols = unlist(mget(probes, hugene10sttranscriptclusterSYMBOL, ifnotfound=NA)) ???????????
Entrez_IDs = unlist(mget(probes, hugene10sttranscriptclusterENTREZID, ifnotfound=NA)) ????????

rma=cbind(probes,Symbols,Entrez_IDs,rma)
write.table(rma, file = "rma.txt", quote = FALSE, sep = "\t", row.names = FALSE, col.names = TRUE)

biocLite("hugene10stprobeset.db") ????????????
biocLite("hugene10sttranscriptcluster.db") ???????

library(hugene10stprobeset.db) ?????????
library(hugene10sttranscriptcluster.db) ?????

These lines do nothing. I don't think that there is a package called citrus.db.

raw.data=ReadAffy(verbose=TRUE, filenames=cels, cdfname="hugene10stv1") ??????
raw.data=ReadAffy(verbose=TRUE, filenames=cels, cdfname="citruscdf")

ls("package:hugene10stprobeset.db") #Annotations at the exon probeset level?????????
ls("package:hugene10sttranscriptcluster.db") ??????????????

do nothing. this is to view the content/ functions of the package.

Symbols = unlist(mget(probes, hugene10sttranscriptclusterSYMBOL, ifnotfound=NA)) ???????????

This is to get the gene symbols. I don't know how to get for citrus

Entrez_IDs = unlist(mget(probes, hugene10sttranscriptclusterENTREZID, ifnotfound=NA)) ????????

This is to get the Entrez Ids. I don't know how to get for citrus