Dear List: 

 

We have a question about obtaining quality control statistics from
library 'simpleaffy'.  

 

We are working on differential gene expression analyses for six files
using the soybean genome (3 Hawaii/Resistant vs. 3 Taiwan/Susceptible).
We successfully read in the .CEL files and obtained the following
AffyBatch object, which contains 61,170 affyids.  

 

> 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

 

As we are interested only in the 'Glycine max' subset which corresponds
to the geneNames for the soybean genome, we followed procedures
(generously supplied by Dr. Jenny Drnevich) and extracted those genes of
interest.  This results in the following updated AffyBatch object of the
same name, soy.ab, which contains only (the correct) 37,744 affyids. 

 

> soy.ab

AffyBatch object

size of arrays=1164x1164 features (63516 kb)

cdf=Soybean (37744 affyids)

number of samples=6

number of genes=37744

annotation=soybean

 

We then attempted to load the library 'simpleaffy' and obtain an object
named 'soy.ab.qc' with the following commands:

 

> library('simpleaffy') 

Loading required package: genefilter

Loading required package: survival

Loading required package: splines

 

Attaching package: 'simpleaffy'

 

 

        The following object(s) are masked _by_ .GlobalEnv :

 

         getBioC 

 

 

Then, in attempting to construct the soy.ab.qc object, we obtained:

 

> soy.ab.qc <- qc(soy.ab) 

Background correcting

Retrieving data from AffyBatch...done.

Computing expression calls... 

......done.

scaling to a TGT of 100 ...

Scale factor for: hr.a5.24 0.410934556631521 

Scale factor for: hr.b5.24 0.236518276485241 

Scale factor for: hr.c5.24 0.265672825818162 

Scale factor for: ts.a6.24 1.96443561512830 

Scale factor for: ts.b6.24 0.320822770974345 

Scale factor for: ts.c6.24 0.334603048637387 

Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about
chip type: soybeancdf

 

We received the error message above, indicating that qc.affy does not
recognize chip type soybeancdf.  Further queries show that the soy.ab.qc
object does not exist at this point.   

 

Can anyone help us to successfully obtain the soy.ab.qc object such that
avbg(...), sfs(...), percent.present(...), ratios(...), etc. may be
used?

 

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

Post Office Box B 

Frederick, MD 21702-1201

Phone: 301.846.5101

Facsimile: 301.846.6196

E-Mail gwa@css.ncifcrf.gov <mailto:gwa@css.ncifcrf.gov> 

 

 


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