[BioC] Resend: altcdfenvs: mapping probes and creating new probe sets: guidance requested

[Ariel Grostern]

Hello,
I am using R 2.10.0. The sessionInfo data is below at the end of this 
message. I am using Ubuntu 10.04.
I am attempting to re-annotate custom Affy PM-only chip using a new 
gene-annotation for my prokaryotic genome. I have gotten stuck on 
altcdfenvs, however.
What I have done so far:
1. Changed the makeProbePackage code to not require MM probe data
2. Created a probe package from my probe_tab file with makeProbePackage (for 
some reason 4800 probes did not match between the probe_tab file and the 
Affy-supplied .CDF file)
3. Installed the new probe package with help from James MacDonald
4. Started following the altcdfenvs documentation....selected the 
constituting elemets, matched the probes.... Everything went smoothly until 
match analysis:
> alt.cdf <- buildCdfEnv.biostrings(m, nrow.chip = 330, ncol.chip = 330)
Warning message:
In buildCdfEnv.biostrings(m, nrow.chip = 330, ncol.chip = 330) :
  Check index for MM probes.

I assumed that the geometry of my chip is 330 x 330, as these are the 
largest X and Y values in the original probe_tab file.
I don't know why i got the MM probes error.
Also, I find that the altcdfenvs documentation becomes much less 
understandable from this point on.....I don't know what to do with 
validAffyBatch(abatch, alt.cdf), etc....where does abatch come from?
If you can point me to any informative discussions on how to proceed, I'd 
really appreciate it. Sorry for the newbie questions.

Ariel Grostern
UC Berkeley




R version 2.10.1 (2009-12-14)
x86_64-pc-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] Rgraphviz_1.24.0         cb1190a520768fprobe_1.0 
cb1190a520768fcdf_1.24.0
 [4] altcdfenvs_2.8.0         hypergraph_1.18.0        graph_1.24.4
 [7] makecdfenv_1.24.0        affyio_1.14.0            matchprobes_1.18.0
[10] Biostrings_2.14.12       IRanges_1.4.16           AnnotationDbi_1.14.1
[13] affy_1.24.2              Biobase_2.6.1

loaded via a namespace (and not attached):
[1] DBI_0.2-5            preprocessCore_1.8.0 RSQLite_0.9-2
[4] tools_2.10.1