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