Question: normilization with RMA, human versus citrus
1
A • 3.8k wrote:
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 resulrt 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") 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") ?????? | |
| 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)) ???????? | |
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| rma=cbind(probes,Symbols,Entrez_IDs,rma) | |
| write.table(rma, file = "rma.txt", quote = FALSE, sep = "\t", row.names = FALSE, col.names = TRUE) |
