Entering edit mode
Marcelo Luiz de Laia
▴
770
@marcelo-luiz-de-laia-377
Last seen 10.2 years ago
Hi everyone.
I am trying to create an object exprSet using the function
read.exprSet and
I am not obtaining success.
I already tried in several ways.
1.) Firts
>
KarinaSusc<-read.table("Ka_Susc.txt",header=TRUE,sep="\t",as.is=TRUE)
> testFile <- tempfile()
> write.table(KarinaSusc, testFile, quote = FALSE, sep = "\t",
row.names
+ =TRUE, col.names = TRUE)
> eSet <- read.exprSet(testFile)
> eSet
Expression Set (exprSet) with
7150 genes
7 samples
phenoData object with 1 variables and 7 cases
varLabels
sample: arbitrary numbering
2.) Second
>
KarinaSusc<-read.table("Ka_Susc.txt",header=TRUE,row.names=1,sep="\t",
as.is=
TRUE)
Error in "row.names<-.data.frame"(`*tmp*`, value = row.names) :
duplicate row.names are not allowed
*** I have the genes duplicate in the file (my nylon filter membrane
had
genes duplicate)
3.) Third
> eSet <- read.exprSet("Ka_Susc.txt")
> eSet
Expression Set (exprSet) with
7150 genes
7 samples
phenoData object with 1 variables and 7 cases
varLabels
sample: arbitrary numbering
> pData(eSet)
sample
Gene 1 * this note is a sample! this is my colunm with the genes
names
SC1 2
SC2 3
SC3 4
ST1 5
ST2 6
ST3 7
4.) Fourth
> read.phenoData("Ka_Susc.txt")
phenoData object with 7 variables and 7151 cases
varLabels
V1: read from file
V2: read from file
V3: read from file
V4: read from file
V5: read from file
V6: read from file
V7: read from file
I have 7150 genes and the 6 variables.
I exported the exprSet "lymphoma" for a file txt and I compared with
the one
that I had created above and I could verify that they are different.
How can I proceed to create an exprSet starting from my file of data?
I have another file with 3575 genes (the average of the duplicates)
My datafile is like this:
Gene_ID SC1 SC2 SC3 ST1 ST2 ST3
gene1 30.2 1.9 32.2 7.4 1.1 8.4
gene2 ...
SC1 = Untreated Replicate 1
SC2 = Untreated Replicate 2
SC3 = Untreated Replicate 3
ST1 = Treated Replicate 1
ST2 = Treated Replicate 2
ST3 = Treated Replicate 3
Thnaks very much
Marcelo Luiz de Laia, M.Sc.
Dep. de Tecnologia, Lab. Bioqu?mica e de Biologia Molecular
Universidade Estadual Paulista - UNESP
Via de Acesso Prof. Paulo Donato Castelane, Km 05
14.884-900 - Jaboticabal, SP, Brazil
PhoneFax: 16 3209-2675/2676/2677 R. 202/208/203 (trab.)
Phone res: 16 3203 2328 - www.lbm.fcav.unesp.br - mlaia@yahoo.com
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