FYI to bioconductor@stat.math.ethz.ch regarding earlier queries. 

 

Hi Greg,

 

yes, in order to read CEL data probeset by probeset (unit==probeset) the
corresponding CDF file must be available.  There is no concept of
probesets in a CEL file; it only contains the (x,y) location of the
probes.  The CDF file maps probesets to (x,y) coordinates.  For your
conveniency, you do not have to specify the CDF file each time you call
readCelUnits().  Instead, affxparser queries the CEL file for the "chip
type" and uses findCdf() to locate the corresponding CDF file. See
?findCdf how to setup the CDF path.  Affymetrix provides most of their
CDF files online (packed up in "library" files).

 

Cheers

 

Henrik

 

PS. If you think your questions are of general interest, which I believe
this one is, it may be better if you ask it through the bioconductor
mailing list, because then my answers can be shared with others too. DS.

 

On 6/29/06, Alvord, Greg (DMS) [Contr] <gwa@css.ncifcrf.gov> wrote:

>

>

>

>

>             Hi Henrick -

>

>

>

>             We made a lot of progress from your suggestion.  I 

> downloaded the 'affxparser' package and successfully acquired the 

> units vector, i.e., > readCelUnits(filenames, units = ...).  

> Unfortunately, this failed (I think) because we were reading in the 

> .CEL files (the only ones available at this

> time) instead of the CDF files.  We tried a few commands to try to get
the

> CDF files, but that did not work.

>

>

>

>             We are currently trying to get back in touch with 

> investigator to see if she can provide me with the CDF files.  I get 

> the impression that that is the next step.

 

>             Thanks again,

>

>                         Greg

 

> -----Original Message-----

>  From: Alvord, Greg (DMS) [Contr]

>  Sent: Thursday, June 29, 2006 12:56 PM

>  To: henrik.bengtsson@gmail.com; hb@stat.berkely.edu

>  Cc: Alvord, Greg (DMS) [Contr]

>  Subject: RE:[BioC] How to read a subset of the .CEL files

>

>

>

>             Henrik -

 

>             Thank you very much for responding to my query regarding 

> how to read a subset of the .CEL files to extract only a portion of 

> the genes

> (affyids) of interest.  I was out of my office for a few days and did
not

> respond immediately.  Thanks again.

 

>             I plan to take your suggestion and work on it sometime 

> this afternoon.  Is the 'affxparser' package something I must download


> from the net, or is it in one of the Bioconductor packages?  I just 

> did a

> ls('package:affy') and could not find it in that package.

>

>

>

>             Anyway, thanks again.  I'm trying to learn.

>

>

>

>             Greg

>

>

See the affxparser package, e.g. readCelUnits(filenames,
units=c(1,600:612,45)).  At the moment,you have to take it from there
yourself.

 

/Henrik Bengtsson

 

On 6/23/06, Alvord, Greg (DMS) [Contr] <gwa@css.ncifcrf.gov> wrote:

>

>

> Dear List -

>

>

>

> I am new to BioConductor and R, working under Windows with a gig of 

> RAM, version R-2.2.1 of R.  I have successfully read in six .CEL files


> and created the following AffyBatch object.

>

>

>

> > soy.ab

>

> AffyBatch object

>

> size of arrays=1164x1164 features (63516 kb)

>

> cdf=Soybean (61170 affyids)

>

> number of samples=6

>

> number of genes=61170

>

> annotation=soybean

>

>

>

> The investigator for whom I'm working is interested in an analysis of 

> differential gene expression on a subset of affyids in this AffyBatch 

> object, specifically in 37,744 of the 61,170 affyids (indicated above)


> that relate specifically to the soybean genome.  I have learned that 

> the relevant species of interest is labeled 'Glycine max'.  I obtained


> this information from another source and have not (due to my 

> ignorance) been able to identify any slot in soy.ab AffyBatch object 

> that identifies this species.  Here is a table of the species on the 

> soy.ab AffyBatch object (which I obtained from another source).

>

>

>

> > cbind(table(Species))

>

>                                           [,1]

>

> Alfalfa mosaic virus                         3

>

> Bean pod mottle virus strain G-7             2

>

> Bean pod mottle virus strain K-Hancock1      1

>

> Clover yellow vein virus                     1

>

> Glycine max                              37744

>

> Heterodera glycines                       7539

>

> Phytophthora sojae                       15864

>

> S. saman                                     4

>

> Southern bean mosaic virus strain SBMV-S     1

>

> Soybean mosaic virus                         1

>

> Soybean mosaic virus strain G5               3

>

> Soybean mosaic virus strain G7               1

>

> Soybean mosaic virus strain N                1

>

> Tobacco ringspot virus                       2

>

> Tobacco streak virus                         3

>

>

>

>

>

> I want to select from the soy.ab AffyBatch object the relevant 

> information for the species 'Glycine max' only.  I have created a data


> frame containing those Affy.ID's for species 'Glycine max', e.g.,

>

>

>

> > Glycine.max.Species.AffyID.df[c(1:3,37742:37744),]

>

>           Species                Affy.ID

>

> 8     Glycine max         AFFX-BioB-3_at

>

> 9     Glycine max         AFFX-BioB-5_at

>

> 10    Glycine max         AFFX-BioB-M_at

>

> 37749 Glycine max soybean_rRNA_838_RC_at

>

> 37750 Glycine max    soybean_rRNA_918_at

>

> 37751 Glycine max soybean_rRNA_918_RC_at

>

>

>

> > dim(Glycine.max.Species.AffyID.df)

>

> [1] 37744     2

>

>

>

> How do I extract/create an AffyBatch object containing only the 

> appropriate Affy.ID's related to the 'Glycine max' species?

>

>

>

> Thank you very much in advance.

>

>             Greg

 

>         [[alternative HTML version deleted]]

>

> _______________________________________________

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>

>

 

 

 

W. Gregory Alvord, Ph.D.

Director, Statistical Consulting Services

Computer and Statistical Services

National Cancer Institute at Frederick

Fort Detrick at 7th Street

Post Office Box B

Miller Drive, Building 362, Room 33

Frederick, MD  21702-1201

Phone:  301.846.5101

Fax:  301.846.6196

E-mail:  gwa@css.ncifcrf.gov

 


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