Hi all. I have a question about something that puzzles me. 
 
I have a set of genes in an index vector that I am interested in.
######################################
> de.idx.Avs
  RG89-F4  RG249-E4  RG317-E7   RG18-B1  RG130-F1   RG88-E1  RG301-B5 
      856      2528      2666      3413      3638      4226      6687 
 RG279-A2  RG121-A5  RG145-A8  RG205-A2   RG18-F2  RG90-B11  RG170-F8 
     7313      7679      7729      7845      8822      8971      9130 
RG248-E11   RG18-A2   RG42-A2   RG94-A5  RG306-A5 RG299-F12   RG89-F3 
     9960     10173     10221     10327     10751     11416     11670 
 RG289-B9   RG7-A12   RG31-A3 RG243-E12  RG265-E3  RG305-A6   RG64-B9 
    12073     12183     12225     12656     13374     13455     13645 
 RG200-F3   RG95-C1   RG95-G7 RG211-C10  RG283-G4  RG88-D10  RG122-D1 
    13914     17761     17766     17999     18140     19103     19845 
RG202-H10  RG206-D7 RG124-C10 RG252-C10   RG18-C1   RG22-G1   RG22-G4 
    20012     20017     20527     20783     20989     20998     21000 
RG238-G10  RG147-H5  RG283-H2  RG185-H2   RG95-C2 RG215-C11  RG231-G2 
    21436     21924     22194     22678     23169     23415     23442 
  RG97-C2 RG145-C11   RG16-D8  RG184-D2 RG202-H11  RG120-C8  RG220-C8 
    23853     23955     24365     24697     25420     25925     26125 
 RG261-D3  RG305-H3   RG7-C12   RG95-G3   RG95-G6  RG151-C3  RG231-G3 
    28237     28326     28407     28578     28580     28689     28850 
 RG293-C9   RG18-D3  RG230-H9   RG18-C3  RG170-G6 
    29657     30453     30882     31805     32112
######################################
 
The names in the vector are the unique identifiers on the chip and the
number is the location on the chip.
 
If I use my home-brewed package to this chip and retrieve geneIDs and
accessionnumbers I use:
 
######################################
Vec.Acc <- unlist(mget(names(de.idx.Avs),Hum30kbatch1to5ACCNUM))
Vec.GeneN <- unlist(mget(names(de.idx.Avs),Hum30kbatch1to5GENENAME))
######################################
 
But if I look at the length of those vectors:
######################################
> length(Vec.Acc)
[1] 68
> length(Vec.GeneN)
[1] 69
######################################
They are not of the same length. I think this depends on some error in the
annotation, because if I just look at the 4:th item in the names(de.idx.Avs)
vector
Its:
######################################
> names(de.idx.Avs)[4]
[1] "RG18-B1"
> names(unlist(mget(names(de.idx.Avs[4]),Hum30kbatch1to5ACCNUM)))
[1] "RG18-B1"
> names(unlist(mget(names(de.idx.Avs[4]),Hum30kbatch1to5GENENAME)))
[1] "RG18-B11" "RG18-B12"
######################################
 
Then two items are returned from the Hum30kbatch1to5GENENAME environment but
only one from the Hum30kbatch1to5ACCNUM environment. I would guess it had
something to do with the mget functions discriminatory ability between
"RG18-B1" and "RG18-B12" or "RG18-B11" but since it works for
Hum30kbatch1to5ACCNUM I do not know. 
 
What also puzzles me is that
 
######################################
> unlist(mget("RG18-B1",Hum30kbatch1to5GENENAME))
                                                                    RG18-B11

"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"

                                                                    RG18-B12

                                                      " translocated to, 10"

######################################
> unlist(mget("RG18-B11",Hum30kbatch1to5GENENAME))
                                  RG18-B11 
"multiple coagulation factor deficiency 2" 
######################################
> unlist(mget("RG18-B12",Hum30kbatch1to5GENENAME))
       RG18-B12 
"transportin 1"
######################################
 
Different GENENAME:s are returned for "RG18-B11" depending if I use
"RG18-B1" or "RG18-B11".
 
Any advice someone?
 
Best regards
 
// Johan L
 
 
 
 
> sessionInfo()
R version 2.1.1, 2005-06-20, i386-pc-mingw32 
 
attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics" 
[6] "grDevices" "utils"     "datasets"  "base"     
 
other attached packages:
         marray        hgu95av2         GOstats        multtest 
        "1.6.3"         "1.8.4"         "1.1.1"         "1.7.3" 
     genefilter        survival          xtable            RBGL 
        "1.6.3"          "2.18"         "1.2-5"        "1.3.13" 
          graph           Ruuid         cluster Hum30kbatch1to5 
        "1.5.9"         "1.5.3"        "1.10.0"         "1.1.0" 
    hgu133plus2         annaffy            KEGG              GO 
        "1.7.0"        "1.0.18"         "1.8.1"         "1.8.2" 
          gcrma     matchprobes            affy         maanova 
        "1.1.4"        "1.0.22"         "1.6.7"        "0.98-3" 
            kth           aroma            R.io      R.graphics 
        "0.4.5"          "0.85"          "0.62"          "0.62" 
       R.colors         R.basic         R.utils            R.oo 
          "0.4"          "0.62"          "0.62"          "0.62" 
          limma      reposTools        annotate         Biobase 
        "2.0.3"        "1.5.19"        "1.5.16"        "1.5.12"

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