[R] Ask for help on the preprocessing of GEO microarray data with Oligo

[Bert Gunter]

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 using 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
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>
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