[rmaexpress_help] Re: == Help to read in CEL file in RMAExpress ==
- From: Ben Bolstad <bmb@xxxxxxxxxxxxx>
- To: rmaexpress_help@xxxxxxxxxxxxx
- Date: Mon, 09 Jul 2007 07:16:54 -0700
You will most likely be able to read the data into R/Bioconductor and
you could certainly use the normalize.quantiles() function as applied to
a matrix using the standard affy package (but pretty much everything
else would be broken for tiling arrays). The newer oligo package might
have more support for tiling array data, but I don't know the specifics
of its support.
Ben
On Sun, 2007-07-08 at 22:41 -0500, mqwu@xxxxxxxxxxxxx wrote:
> I hate to bother you again, but I think u can give me quick clue. Do you
> know if Bioconductor support Tiling array data? or I have to write code to
> normalize according to your 2003 paper?
>
> Sincerely,
> -------
> Mingqi
> Email:mqwu@xxxxxxxxxxxxx
>
> > The short answer is the current version of RMAExpress only supports 3'
> > expression arrays and also the newer Exon arrays.
> >
> > Tiling array data is not currently supported.
> >
> > Ben
> >
> >
> >
> >
> > On Sun, 2007-07-08 at 18:52 -0500, Mingqi Wu wrote:
> >> Dear All,
> >>
> >> I am new to RMAexpress. I am trying to use RMAExpress to normalize CEL
> >> data file from Affymetrix GeneChip microarrays.
> >>
> >> I have installed RMAExpress 0.5 on my windows XP, however I met 2
> >> problem:
> >>
> >> 1. I can not load CEL file: File -> Read Unprocess Files -> CDF files
> >> (there is only one option for CDF file, no CEL option)
> >>
> >> 2. I tried to convert the CEL file with RMADataConv. I first choose CEL
> >> File Dir, then set Output dir and choose Convert, it always saying could
> >> not read CEL file.
> >>
> >> By the way, I use a public CEL file from following link:
> >>
> >> http://transcriptome.affymetrix.com/publication/tfbs/
> >>
> >> *Transcription Factor Binding Sites Data*
> >>
> >> * Raw CEL Data
> >>
> >> <http://transcriptome.affymetrix.com/download/publication/tfbs_data/intensity/cel.tgz>.
> >>
> >>
> >>
> >> Could you give me some help? is the data problem or RMAexpress prolbem?
> >>
> >> Thank you so much.
> >>
> >> Sincerely,
> >> -----------
> >> Mingqi Wu
> >> Email: mqwu@xxxxxxxxxxxxx
> >>
> >
> >
>
>
>
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