[BioC] (no subject)

[rkakkar at uchicago.edu]

i am trying to import a probe list into R for use in annaffy. 

i have used affy to generate an eset which i imported into SAM (MS Excel).   
After SAM permutation, I now have a list of probe ids (a csv 
file "probelist.csv") that id like to bring back into bioconductor to 
annotate.  i created an object "sam" as follows: 

>sam <- read.csv("probelist.csv") 
to bring the probe list into R ("probelist.csv" is one column, only the probe 
ids).  i am trying to follow the annaffy primer vignette but cant get my list 
("sam") in the proper format for aafTableAnn to read. 

i am posting my inputs and the error output below which lead me to belive this 
is an improper object issue, ie my list "sam" is not the right type of object, 
not the same object as "probeids" as depicted in the vignette. 

obliged. 


> sam<-read.csv("probelist.csv", header=FALSE) 
> sam 
             V1 
1    1448553_at 
2    1450791_at 
3  1438651_a_at 
4    1417065_at 
5    1452661_at 
6    1415801_at 
7    1433575_at 
8    1422562_at 
9  1452417_x_at 
10   1416805_at 
11 1427883_a_at 
12   1418403_at 
13   1423606_at 
14   1448201_at 
15 1427868_x_at 
16   1427884_at 
17 1427520_a_at 
18 1456700_x_at 
19   1415800_at 
20 1442025_a_at 
21   1428942_at 
22   1424211_at 
23   1416125_at 
24 1419874_x_at 
25   1452418_at 
26   1448185_at 
27 1435626_a_at 
28 1453238_s_at 
29   1423405_at 
30   1442026_at 
31   1417266_at 
32   1418901_at 
33 1422557_s_at 
34 1417968_a_at 
35   1427638_at 
36   1450974_at 
37   1416225_at 
38   1437061_at 
39   1448231_at 
40   1448181_at 
41 1433711_s_at 
42   1448647_at 
43   1418174_at 
44   1427202_at 
45   1418003_at 
46   1451069_at 
47 1427844_a_at 
48   1448756_at 
49   1425515_at 
50   1449335_at 
51 1438211_s_at 
52   1427126_at 
53   1427384_at 
54 1425837_a_at 
55   1448898_at 
56   1429379_at 
57 1449901_a_at 
58 1417168_a_at 
59   1425514_at 
60   1451006_at 
61   1434832_at 
62 1419394_s_at 
63   1434010_at 
64   1417936_at 
65   1419144_at 
66 1427127_x_at 
> anncols 
 [1] "Probe"               "Symbol"              "Description"         
 [4] "Function"            "Chromosome"          "Chromosome Location" 
 [7] "GenBank"             "LocusLink"           "Cytoband"           
[10] "UniGene"             "PubMed"              "Gene Ontology"       
[13] "Pathway"             
> anntable<-aafTableAnn(sam, "moe430a", anncols) 
Error in validObject(.Object) : Invalid "aafTable" object: Invalid object for 
slot "probeids" in class "aafTable": got class "data.frame", should be or 
extend class "character" 
>