Question: Reading in .gpr files
0
gravatar for english.server
16 months ago by
english.server0 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 • 270 views
ADD COMMENTlink modified 16 months ago by Gordon Smyth37k • written 16 months ago by english.server0

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 16 months ago • written 16 months ago by Gordon Smyth37k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 156 users visited in the last hour