[BioC] question in read.exprSet and read.phenoData

Marcelo Luiz de Laia mlaia at fcav.unesp.br
Sun Nov 2 16:44:50 MET 2003


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. Bioquímica 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 at yahoo.com
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