Dear List,

I have questions about Simpleaffy session in R&Bioconductor Manual,
http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html#biocon_simpleaffy
.

I used 6 .cel files for test and created the corresponding *covdesc.txtfile.

*I had no problem with ''Creating expression values from CEL files''. For
the 2nd step "Quality control steps",
when I ran:
qc <- qc(x,x.mas5)

The error message was:
> qc <- qc(x,x.mas5)
error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip
type: hthgu133acdf

even if I loaded hthgu133acdf package, nothing changed:

> library(hthgu133acdf)
> qc <- qc(x,x.mas5)
error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip
type: hthgu133acdf
>

Then I had to skip the rest codes in that step.

When I proceeded to Step3 Filtering by expression values, I first ran:
*get.array.subset(x.rma, "treatment",c("CMP1","Ctrl"))
*and then:
*results <- pairwise.comparison(x.rma, "treatment", c("1", "2"), raw.data)**
*
The error message I got is:

> results <- pairwise.comparison(x.rma, "treatment", c("1", "2"), raw.data)
error in if (alpha1 < 0) { : The missing value can not be used where
TRUE/FALSE is required

I have no clue about this but I am curious about if I should replace
c("1","2") with c("CMP1","Ctrl")?

I really appreciate your help so that I can move the analysis forward.

Thank you!

Sincerely,

Alex

	[[alternative HTML version deleted]]

