 

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 

 

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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