Question: normilization with RMA, human versus citrus
1
gravatar for F
4.1 years ago by
F3.4k
Iran
F3.4k 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)) ????????
   
 

 

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

 

   

 

rma affy r microarray • 1.3k views
ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by F3.4k
3
gravatar for Deepak Tanwar
4.1 years ago by
Deepak Tanwar4.0k
ETH Zürich, Switzerland
Deepak Tanwar4.0k wrote:
biocLite("hugene10stprobeset.db") ????????????

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



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

library(hugene10sttranscriptcluster.db) ?????

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

ADD COMMENTlink written 4.1 years ago by Deepak Tanwar4.0k
0
gravatar for F
4.1 years ago by
F3.4k
Iran
F3.4k wrote:

thank you Deepak,

when i did normlization with my doupts i got a rma.txt like below, a long file ( one column and many rows) of which i cpoied and pasted only few rows:

GSM1645665_120727-120222A_H_Citrus_.CEL
 1.7350
 1.7350
 6.5272
 6.7832
 6.9627
 7.8931
 7.8896
10.3757
 9.4220
11.4562
 8.4377
 9.7743
 8.3431
 8.2561
 9.3874
 7.8312
 8.7202
 5.5769
 5.5464
 5.7477
 6.1443
 5.4833
 6.2989
 7.7261
 5.9480
 6.6255
 6.8168
 6.8916

while the produced rma.txt by tutorial is like this:

#%guid=00003123-44eb-4068-1f22-004e560061c2
#%affymetrix-algorithm-param-apt-engine=ProbesetSummarizeEngine
#%affymetrix-algorithm-param-apt-program-name=Expression Console
#%affymetrix-algorithm-param-apt-command-line=
#%affymetrix-algorithm-param-apt-exec-guid=0000040472-1431761500-0000017680-0000004998-0000023182
#%affymetrix-algorithm-param-apt-analysis-guid=0000758a-0436-4e15-2043-004609003cbb
#%affymetrix-algorithm-param-apt-time-str=Sat May 16 12:01:40 2015
#%affymetrix-algorithm-param-apt-version=1.4.1.46
#%affymetrix-algorithm-param-apt-cvs-id=.........................................................

i think by my doubts i could not get the proper result

 

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by F3.4k
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