Question: Reading in .gpr files
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gravatar for english.server
20 months ago by
english.server20 wrote:

Hi everyone!

 

I need to read in .gpr files downloaded from GEO. I cant get either read.maimages {limma} or read.GenePix {marray} working. Where am I wrong? Thank you inn advance.

files= dir()
files= files [grep(files, pattern = '*.gpr$')]
library (limma) #1
library (marray) #2
data=   read.maimages(files, green.only=T, columns= list(c('F532 Median','B532 Median')))
data=   read.maimages(files, green.only=T,source='genepix')
data= read.GenePix (files, name.Gf='F532 Median', name.Gb = 'B532 Median')
microarray • 326 views
ADD COMMENTlink modified 20 months ago by Gordon Smyth39k • written 20 months ago by english.server20

Well, the first call to read.maimages() couldn't possibly work, because columnsalways has to be a list with named components (as the help page says!). Perhaps you intended columns = list(Gf = "F532 Median", Gb = "B532 Median").

Anyway, please tell us what the error messages were. Also, which GEO series are you trying to read?

ADD REPLYlink modified 20 months ago • written 20 months ago by Gordon Smyth39k
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