hi friends,

i need your help please...i tried to adopt a tutorial in human (GSE27447) to my case in citrus sinensis because i am not familiar enough with R...

 but 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")       biocLite("citruscdf")
biocLite("hugene10stv1probe")  biocLite("citrusprobe")
biocLite("hugene10stprobeset.db")  ????????????
biocLite("hugene10sttranscriptcluster.db") ???????

library(GEOquery)
library(affy)
library(gcrma)
library(hugene10stv1cdf)   library("citruscdf")
library(hugene10stv1probe) 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")
raw.data=ReadAffy(verbose=TRUE, filenames=cels, cdfname="hugene10stv1") ("citruscdf")

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") ??????
#Extract probe ids, entrez symbols, and entrez ids
probes=row.names(rma)
Symbols = unlist(mget(probes, hugene10sttranscriptclusterSYMBOL, ifnotfound=NA)) ?????
Entrez_IDs = unlist(mget(probes, hugene10sttranscriptclusterENTREZID, ifnotfound=NA)) ???

#Combine gene annotations with raw data
rma=cbind(probes,Symbols,Entrez_IDs,rma)

#Write RMA-normalized, mapped data to file
write.table(rma, file = "rma.txt", quote = FALSE, sep = "\t", row.names = FALSE, col.names = TRUE)

There is no annotation package for this array, so you will have to use the file available from GEO, or get the annotation file from Affy. You don't have to tell the affy package what files it needs, this will suffice:

raw.data=ReadAffy(verbose=TRUE, filenames=cels)

and then you can summarize using

eset <- rma(raw.data)

then you can get annotation using GEOquery:

annot <- getGEO("GPL5731")

annot <- Table(annot)

You will probably have to look at the annotation data to see what you want to use, and then you can use merge() to make a data.frame that you can write out.

thank you very much

sorry James;

when i did these steps and used the rma.txt as input to aracne, it said that "no microarray name provided...

what does this error mean please?

thanks a lot James for your attention,you are all right

i normalized an array experiment with RMA then the output was a rma.txt which i used as an input in ARACNe that i got error because i should select tab delimited format from menu because rma.txt was in this format....today i tried many hour to understand the reason of error.

anyway i am thankful