Well, I've struggled quite a bit over the past several weeks to come up with a viable way to make an annaffy-compatible annotation package for the relatively new Affymetrix Yeast 2.0 chip. So far, in spite of everyone's generous help and tips, I haven't been successful. I've gotten the closest to making it work by using yeastann and yeastPkgBuilder within AnnBuilder, but the data that's built just contains a bunch of "NA"s for everything but the probe ids and the SGD accession numbers (both of which I gave in the input file). I'm unable to find the orf numbers required by yeastPkgBuilder, but I gave it a shot with the SGD accession numbers (which is really all I have to work with). Obviously, it didn't work. Anyway, then I figured I might as well at least try to use the current YEAST annotation, to see how much of the Yeast 2.0 chip it covers. I used aafSearchText (via annaffy in webbioc) to search for a list of probes from the Yeast 2.0 chip. Here's the code and subsequent error message I got: > chip <- "YEAST" > colnames <- c("Probe") > text <- c("1769799_at + 1771363_at + 1779354_at + 1771073_at + 1770610_at + 1779591_at + 1779214_at + 1777292_at + 1779767_at + 1779046_at + 1777723_at") > library(annaffy) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: GO Loading required package: KEGG Loading required package: annotate > probeids <- aafSearchText(chip, colnames, text) Loading required package: YEAST Error in try(name) : Object "YEASTSYMBOL" not found Error in as.environment(pos) : no item called "YEASTSYMBOL" in the search list Execution halted This was also reproducible within the R console (Mac OS X 10.3.7). I built the latest YEAST package from source, and could not find a "YEASTSYMBOL" component anywhere. I'm using R 2.0.1, with annaffy 1.0.11 and the latest YEAST package from the site. Any help? Thanks in advance, Jake Michaelson

Jacob Michaelson wrote: > Well, I've struggled quite a bit over the past several weeks to come up > with a viable way to make an annaffy-compatible annotation package for > the relatively new Affymetrix Yeast 2.0 chip. > > So far, in spite of everyone's generous help and tips, I haven't been > successful. I've gotten the closest to making it work by using yeastann > and yeastPkgBuilder within AnnBuilder, but the data that's built just > contains a bunch of "NA"s for everything but the probe ids and the SGD > accession numbers (both of which I gave in the input file). I'm unable > to find the orf numbers required by yeastPkgBuilder, but I gave it a > shot with the SGD accession numbers (which is really all I have to work > with). Obviously, it didn't work. > > Anyway, then I figured I might as well at least try to use the current > YEAST annotation, to see how much of the Yeast 2.0 chip it covers. I > used aafSearchText (via annaffy in webbioc) to search for a list of > probes from the Yeast 2.0 chip. Here's the code and subsequent error I don't think you will be able to use annaffy with the YEAST package. You may well need to do things more by hand. Here are some quick pointers. To see what is in the YEAST package: > library(YEAST) > YEAST() Quality control information for YEAST Date built: Thu Jan 6 10:38:43 2005 Number of probes: 5799 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: YEASTALIAS found 1738 of 5799 YEASTCHRLOC found 5799 of 5799 YEASTCHR found 5799 of 5799 YEASTDESCRIPTION found 5742 of 5799 YEASTENZYME found 790 of 5799 YEASTGENENAME found 4331 of 5799 YEASTGO found 5798 of 5799 YEASTPATH found 1138 of 5799 YEASTPMID found 5544 of 5799 Mappings found for non-probe based rda files: YEASTCHRLENGTHS found 17 YEASTENZYME2PROBE found 438 YEASTGO2ALLPROBES found 3517 YEASTGO2PROBE found 2473 YEASTORGANISM found 1 YEASTPATH2PROBE found 101 YEASTPMID2PROBE found 33921 To see what you have to use to query the different hash tables: ls(YEASTALIAS)[1:10] [1] "Q0045" "Q0050" "Q0055" "Q0060" "Q0065" "Q0070" "Q0075" "Q0080" "Q0085" "Q0105" This indicates that you have to pass SGD IDs to get results. To see results for a single SGD ID: > get("Q0045", YEASTDESCRIPTION) [1] "Subunit I of cytochrome c oxidase, which is the terminal member of the mitochondrial inner membrane electron transport chain; one of three mitochondrially-encoded subunits" > get("Q0045", YEASTGENENAME) [1] "COX1" > get("Q0045", YEASTCHRLOC) 17 13818 To get multiple results, use mget(): > mget(ls(YEASTALIAS)[1:5], YEASTGENENAME) $Q0045 [1] "COX1" $Q0050 [1] "AI1" $Q0055 [1] "AI2" $Q0060 [1] "AI3" $Q0065 [1] "AI4" > mget(ls(YEASTALIAS)[1:5], YEASTDESCRIPTION) $Q0045 [1] "Subunit I of cytochrome c oxidase, which is the terminal member of the mitochondrial inner membrane electron transport chain; one of three mitochondrially-encoded subunits" $Q0050 [1] "Reverse transcriptase required for splicing of the COX1 pre-mRNA, encoded by a mobile group II intron within the mitochondrial COX1 gene" $Q0055 [1] "Reverse transcriptase required for splicing of the COX1 pre-mRNA, encoded by a mobile group II intron within the mitochondrial COX1 gene" $Q0060 [1] "Endonuclease I-SceIII, encoded by a mobile group I intron within the mitochondrial COX1 gene" $Q0065 [1] "Endonuclease I-SceII, encoded by a mobile group I intron within the mitochondrial COX1 gene; intron is normally spliced by the BI4p maturase but AI4p can mutate to acquire the same maturase activity" You will probably also want to look at ?lapply, ?sapply, ?unlist. HTH, Jim > message I got : > > chip <- "YEAST" > > colnames <- c("Probe") > > text <- c("1769799_at > + 1771363_at > + 1779354_at > + 1771073_at > + 1770610_at > + 1779591_at > + 1779214_at > + 1777292_at > + 1779767_at > + 1779046_at > + 1777723_at") > > library(annaffy) > Loading required package: Biobase > Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > Loading required package: GO > Loading required package: KEGG > Loading required package: annotate > > probeids <- aafSearchText(chip, colnames, text) > Loading required package: YEAST > Error in try(name) : Object "YEASTSYMBOL" not found > Error in as.environment(pos) : no item called "YEASTSYMBOL" in the > search list > Execution halted > > > This was also reproducible within the R console (Mac OS X 10.3.7). I > built the latest YEAST package from source, and could not find a > "YEASTSYMBOL" component anywhere. > > I'm using R 2.0.1, with annaffy 1.0.11 and the latest YEAST package from > the site. > > Any help? > > Thanks in advance, > > Jake Michaelson > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109

Jacob- The YEAST annotation package is a bit unlike all the others in that it does not include the "*SYMBOL" environment mapping probe set ids onto commonly used abbreviations for genes. In all the other annotation packages, using the "*SYMBOL" environment was an easy way to get a listing of every probe id on the chip. That doesn't work with the YEAST package. There will hopefully be an updated annaffy package which doesn't depend on the "*SYMBOL" environment for Probe searches in the next few days. -Colin On Feb 7, 2005, at 3:00, bioconductor-request@stat.math.ethz.ch wrote: > Well, I've struggled quite a bit over the past several weeks to come up > with a viable way to make an annaffy-compatible annotation package for > the relatively new Affymetrix Yeast 2.0 chip. > > So far, in spite of everyone's generous help and tips, I haven't been > successful. I've gotten the closest to making it work by using > yeastann and yeastPkgBuilder within AnnBuilder, but the data that's > built just contains a bunch of "NA"s for everything but the probe ids > and the SGD accession numbers (both of which I gave in the input file). > I'm unable to find the orf numbers required by yeastPkgBuilder, but I > gave it a shot with the SGD accession numbers (which is really all I > have to work with). Obviously, it didn't work. > > Anyway, then I figured I might as well at least try to use the current > YEAST annotation, to see how much of the Yeast 2.0 chip it covers. I > used aafSearchText (via annaffy in webbioc) to search for a list of > probes from the Yeast 2.0 chip. Here's the code and subsequent error > message I got: >> chip <- "YEAST" >> colnames <- c("Probe") >> text <- c("1769799_at > + 1771363_at > + 1779354_at > + 1771073_at > + 1770610_at > + 1779591_at > + 1779214_at > + 1777292_at > + 1779767_at > + 1779046_at > + 1777723_at") >> library(annaffy) > Loading required package: Biobase > Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > Loading required package: GO > Loading required package: KEGG > Loading required package: annotate >> probeids <- aafSearchText(chip, colnames, text) > Loading required package: YEAST > Error in try(name) : Object "YEASTSYMBOL" not found > Error in as.environment(pos) : no item called "YEASTSYMBOL" in the > search list > Execution halted > > > This was also reproducible within the R console (Mac OS X 10.3.7). I > built the latest YEAST package from source, and could not find a > "YEASTSYMBOL" component anywhere. > > I'm using R 2.0.1, with annaffy 1.0.11 and the latest YEAST package > from the site. > > Any help? > > Thanks in advance, > > Jake Michaelson