[BioC] regarding GCRMA normalization

James MacDonald jmacdon at med.umich.edu
Thu Jan 28 13:05:22 CET 2010

Hi Sneha,

There are going to be several problems for you. First, the getDataAffy() function expects the data to be in a certain format which is obviously being violated here. So you _could_ modify the probe_tab file to conform to that format.

However, a bigger problem is that the chip you are using is a PM-only chip. There are some background probes on the chip, but they are not MM-probes so I don't believe the underlying assumptions for the gcrma model are going to apply.



James W. MacDonald, M.S.
Douglas Lab
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
>>> sneha patil  01/28/10 2:04 AM >>>

i have prepared the HuGene-1_0-st-v1.r3.cdf package...and want to preapare a
probe package....while making the probe package i am getting this
error.....also my probe file is the zip file.,....

> makeProbePackage("Hugene-1_0-st-v1.r3",datafile =
+ outdir = "outdir",maintainer = "me",version = "0.0.1",species =
+ check = FALSE,force = TRUE)
Importing the data.
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
  scan() expected 'an integer', got '+'

plzz help me regarding this

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