[BioC] Problem reading CEL files

Xia Han xia.han at bms.com
Thu May 6 22:07:08 CEST 2004


Hi:

I am trying to use affy package to normalize  79 hgu133a chips. I
have R1.8.1 and affy 1.3 on windows 2000.
I am trying to use justRMA( ) and keep getting error messages
like this:
"Cel file xxxxxx.cel does not seem to be of HG-U133A type".

I stored 79 cel files in a vector called all.cel.files. Here is
what I am getting:
================================================================
> library(affy)
> data <- justRMA(filenames=all.cel.files)
Error in read.probematrix(filenames = filenames) :
        Cel file XH2003031149A.cel does not seem to be of
HG-U133A type
## This is the #46th chip in all my cel files.
> data <-justRMA(filenames=all.cel.files[1:45])
Background correcting
Normalizing
Calculating Expression
## Works fine.
> data1 <- justRMA(filenames=all.cel.files[46:50])
Error in read.probematrix(filenames = filenames) :
        Cel file XH2003030551A.cel does not seem to be of
hg-u133a type
# This is the # 47th chip.
> data1 <- justRMA(filenames=all.cel.files[47:50])
Background correcting
Normalizing
Calculating Expression
# Works again.
================================================================

If I put the problem chip in the position #1 it will be fine, but
there're always other chips ran into the same problem. It's very
strange to me. Even I could do several times justRMA( ) and merge
them together later, I imagine it would not make sense in terms
of  normalization.

Help, please!

Xia



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