[BioC] annaffy: YEAST vs. Affy YEAST_2 annotation

[James W. MacDonald]

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
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109