Question: Reading in .gpr files
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
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 229 users visited in the last hour