Boxplot for Raw Data

Question

[shawin]

I have a micro array data set , and it is Affy, and i read it using the code bellow :

   CuCelfiles<-list.celfiles(full.names=TRUE)
   CuCelfiles
   data<-read.celfiles(CuCelfiles, pkgname="pd.hugene.1.0.st.v1")
   # The box plot dispaly unorganize name of cel file 
   boxplot(data)
   CuNorm<-rma(CuCelfiles)

I would like change the name of cell fise instead of GSE12345 to H1 , i could not do that , i tried to write data to csv but it does not work ? Any help please

[mastal511]

What have you tried?

By the way, the GSE file you mention, GSE12345, and the pkgname in your code, pd.hugene.1.0.st.v1, are both Affymetrix arrays, not agilent. But the GSE12345 study was done with the Affymetrix Human Genome U133 Plus 2.0 Array, not the hugene array.

[shawin]

@mastal511 , Yes sorry for confusion, it is Affy. I have tried write the data to a csv file write.csv(data,"data.csv"); in the csv file i could change the sample names, but it does not work ?

Answer 1

[theobroma22]

First you need to make the annotation file using the pfInfoBuilder package for your Affy celfiles. Then, you can read the celfiles with the annotation, not the package used in the example vignette.

[shawin]

I never used pfInfoBuilder package , please could you elaborate , why i should use this package and how ? when i normalize the data using RMA() method and then write it to csv the output is not like other affy data , the GSE is in the row and the ID is the column ? what i mean it is inverse format ??

[mastal511]

You shouldn't need to use pfInfoBuilder, the annotations for the Affymetrix hgu133plus2 array are available in Bioconductor.

In the code you showed in the original post, you have the name of the wrong array package 'pkgname="pd.hugene.1.0.st.v1"', you should remove that from your code. The read.celfiles function should be able to get the name of the package from the cel files.