how to make "custom" affy batch vector (affymetrix plus2)

Question

[osiemen]

Dear all,

Using the frmatools library in R I would like to create own affybatch Vectors.
I am using the makevectorsaffybatch() function for this but I am receiving the following errors using it:

vec <- makeVectorsAffyBatch(files = listWithCelFiles ,file.dir = fullPathToCelFiles,batch.id = rep(1:200, each = 5))

Error: the following are not valid files: GSM100896.CEL GSM100897.CEL GSM100898.CEL GSM100901.CEL etc...

if I it try this way

vec <- makeVectorsAffyBatch(file.dir = fullPathToCelFiles,batch.id = rep(1:200, each = 5))

I receive the error: Error in setwd(file.dir) : cannot change working directory

I understand that I cannot change the dir while creating vectors. (All the CEL files are in different subdirectorys , so what could I do for this problem? )

But in general I don't why it says that my files are not valid, I unzipped them to use them but when they were zipped i received the same error.

Can anyone help me out or have some tips for me regarding these problems?

Thanks in advance!

Answer 1

[osiemen]

I think i found the answer to this myself .

Unzip al .CEL files in to 1 directory and use this directory to read them in.

setwd("path/to/CEL/files")

celfiles <- dir()

vec <- makeVectorsAffyBatch(celfiles, batch.id ,etc...)

this should work.