R help - Nov 2019 - Ask for help on the preprocessing of GEO microarray data with Oligo

Dear Sir



I have downloaded the raw CEL data included in "GSE41418" from GEO and
tried to process the raw microarray data according to the following Rscripts


  affydata <- ReadAffy(cdfname = "mouse4302mmentrezgcdf")
  eset <- oligo::rma(affydata)



The raw data can be read by ReadAffy but failed in the normalization process. I
have tried to process it with affy::rma, frma::frma and oligo::rma, but it still
can not work. An error saying "address 0x7f854500a000, cause 'invalid
permissions'" was returned. However this error message was not appeared
in some other datasets like "GSE41342". I was wondering whether this
file was corrupted.
Could you please help me address this problem? Any suggestion and recommendation
are welcome.





Best
	[[alternative HTML version deleted]]

My recommendation is:

Post on the BioConductor site, not here.

Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Thu, Nov 14, 2019 at 9:22 AM chziy429 <chziy429 at 163.com> wrote:
> Dear Sir
>
>
>
> I have downloaded the raw CEL data included in "GSE41418" from
GEO and
> tried to process the raw microarray data according to the following
Rscripts
>
>
>   affydata <- ReadAffy(cdfname = "mouse4302mmentrezgcdf")
>   eset <- oligo::rma(affydata)
>
>
>
> The raw data can be read by ReadAffy but failed in the normalization
> process. I have tried to process it with affy::rma, frma::frma and
> oligo::rma, but it still can not work. An error saying "address
> 0x7f854500a000, cause 'invalid permissions'" was returned.
However this
> error message was not appeared in some other datasets like
"GSE41342". I
> was wondering whether this file was corrupted.
> Could you please help me address this problem? Any suggestion and
> recommendation are welcome.
>
>
>
>
>
> Best
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
	[[alternative HTML version deleted]]