[BioC] regarding GCRMA normalization

[James MacDonald]

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.

Best,

Jim


James W. MacDonald, M.S.
Biostatistician
Douglas Lab
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
>>> sneha patil  01/28/10 2:04 AM >>>
hiii,

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 =
gzfile("HuGene-1_0-st-v1.probe.tab",open="r"),
+ outdir = "outdir",maintainer = "me",version = "0.0.1",species =
"Homo_sapiens",
+ 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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