Hi All,

I'm repeating my earlier post below, as it didn't bring any reply.
If you have worked in the mixture CDF environment, I would appreciate if you
could give me some direction, please.

--------
I'm trying to combine hgu133a and hgu133a2 for a single downstream analysis.
It is my first attempt, and have recently come across the idea of the
mixture CDF environment. As I try to move on down this road considering that
this is perhaps "the" option I have, eventually I could only sense that
something is going not in the right direction (as follows).

Any suggestions and advice would indeed be valuable.

Thanks.

Chintanu



> sessionInfo()
R version 2.7.0 (2008-04-22)
i386-pc-mingw32

locale:

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
methods   base

other attached packages:
 [1] hgu133acdf_2.2.0     hgu133aprobe_2.2.0   hgu133a2probe_2.2.0
hgu133a2cdf_2.2.0    matchprobes_1.12.0   MergeMaid_2.12.0     MASS_7.2-41
 [8] survival_2.34-1      affy_1.18.0          preprocessCore_1.2.0
affyio_1.8.0         Biobase_2.0.0


> cdfName(Data_A)                              #  Data_A is ReadAffy () of a
set of CEL files
[1] "HG-U133A"

> cdfName(Data_B)                              #  Data_B is ReadAffy () of
another set of CEL files
[1] "HG-U133A_2"


> comBatch <- combineAffyBatch(list(Data_A, Data_B), c("hgu133aprobe",
"hgu133a2probe"),
newcdf = "hgu133aa2")
package:hgu133aprobe    hgu133aprobe
package:hgu133a2probe   hgu133a2probe
241837 unique probes in common

> Data_C=comBatch$dat
> hgu133aa2cdf=comBatch$cdf

> "@"(Data_C, "cdfName", "hgu133aa2cdf")
[1] "hgu133aa2"
> "@"(Data_C, "cdfName")
[1] "hgu133aa2"


> class (Data_C)                                # Same for Data_A and Data_B
[1] "AffyBatch"
attr(,"package")
[1] "affy"



> summary (Data_C)
  Length     Class      Mode
      20 AffyBatch        S4

> summary (Data_B)
  Length     Class      Mode
       6 AffyBatch        S4

> summary (Data_A)
  Length     Class      Mode
      14 AffyBatch        S4


> show (Data_A)
AffyBatch object
size of arrays=712x712 features (8 kb)
cdf=HG-U133A (22283 affyids)
number of samples=14
number of genes=22283
annotation=hgu133a
notes=

> show (Data_B)
AffyBatch object
size of arrays=732x732 features (8 kb)
cdf=HG-U133A_2 (22277 affyids)
number of samples=6
number of genes=22277
annotation=hgu133a2
notes=


> show (Data_C)
AffyBatch object
size of arrays=0x0 features (8 kb)
cdf=hgu133aa2 (??? affyids)
number of samples=20
Error in getCdfInfo(object) :
 Could not obtain CDF environment, problems encountered:
Specified environment does not contain hgu133aa2
Library - package hgu133aa2cdf not installed
Data for package affy did not contain hgu133aa2cdf
Bioconductor - hgu133aa2cdf not available
In addition: Warning message:
missing cdf environment! in show(AffyBatch)

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