hello bioconductor users,

i am a new user of bioconductor and i am having some trouble using the
simpleaffy package.
i am using the poplar genome arrays.

i encounter the following error when i try to run a pairwise.comparison.
> results.nm6.rma <- pairwise.comparison(nm6.rma, "treatment", c("NM6 1h",
"NM6 13h"), pv.raw.data.nm6)
Error in spots[, is.element(grp, members)] :
        incorrect number of dimensions

i would be most grateful if anyone could offer me any advice on this error.
also, would i be better to use affy for my analysis?

thanks in advance.
olivia

here is everything i encounter up to that point:

> raw.data.nm6 <- read.affy ()
> nm6.rma <- call.exprs(raw.data.nm6, "rma")
Background correcting
Normalizing
Calculating Expression
> pv.raw.data.nm6 <- detection.p.val(raw.data.nm6, alpha1=0.05, alpha2=0.065
)
Getting probe level data...
Computing p-values
Doing PMA Calls
> results.nm6.rma <- pairwise.comparison(nm6.rma, "treatment", c("NM6 1h",
"NM6 13h"), pv.raw.data.nm6)
Error in spots[, is.element(grp, members)] :
        incorrect number of dimensions


(

if i do not do the detection.p.val step this is the result of the
pairwise.comparison

> results.nm6.rma <- pairwise.comparison (nm6.rma, "treatment", c("NM6 1h",
"NM6 13h"), raw.data.nm6)
Error in if (alpha1 < 0) { : missing value where TRUE/FALSE needed
>

)

in this case i have created a dirctory with only 2 treatments, each with 3
reps - 6 .CEL files total.

so i tried to use the other example in the vignette for when there are only
3 treatments. but still i get an error.

> results.nm6.rma <- pairwise.comparison(nm6.rma, "treatment", spots=
pv.raw.data.nm6)
Error in spots[, is.element(grp, members)] :
        incorrect number of dimensions

> sessionInfo()
Version 2.3.1 (2006-06-01)
x86_64-unknown-linux-gnu

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
[7] "utils"     "datasets"  "base"

other attached packages:
 poplarcdf simpleaffy genefilter   survival       affy     affyio    Biobase
  "1.12.0"    "2.6.0"   " 1.10.1"     "2.26"   "1.10.0"    "1.0.0"   "1.10.1
"
>

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