 

            Greetings to all from a newcomer to Bioconductor and R:

 

            I am currently operating version R-2.2.1 under Windows XP
with a gig of RAM. We successfully created and AffyBatch object, soy.ab,
after reading in .CEL files

 

> 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

 

comprising six samples, three replicates of a variety of soybean
inoculated with a fungus to which it was (1) susceptible and, (2) three
to which it was not susceptible (i.e., resistant).  

 

Several of the quality assessment procedures from Chapter 3, "Quality
Assessment of the Affymetrix GeneChip Data", in the (excellent)
Bioinformatics ... R and Bioconductor book with editors Gentlemen et al,
were successfully applied (image plots on the raw and log probe level
data, boxplots, histograms (density plots), MA-plots, and the RNA
degradation plot).  After loading 'simpleaffy' and attempting to apply
the qc function, we get

 

> library('simpleaffy') 

> 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: a3hr 0.840708132971358 

Scale factor for: b3hr 0.462379333292756 

Scale factor for: c3hr 1.00194774416652 

Scale factor for: a4ts 0.65061265407157 

Scale factor for: b4ts 0.904160988759934 

Scale factor for: c4ts 1.11602093572676 

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

 

with the subsequent indication 

 

> soy.ab.qc

Error: object "soy.ab.qc" not found

    

Also after loading 'affyPLM', we get

 

> library('affyPLM') 

Loading required package: affydata

Loading required package: gcrma

Loading required package: matchprobes

> Pset1 <- fitPLM(soy.ab) 

Background correcting PM

Normalizing PM

Error in fitPLM(soy.ab) : negative extents to matrix

> show(Pset1) 

Error: object "Pset1" not found

Error in show(Pset1) : unable to find the argument 'object' in selecting
a method for function 'show'

 

We are grateful to anyone who can help us understand what these errors
mean and how we might circumvent them.

 

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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