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gravatar for rkakkar@uchicago.edu
15.6 years ago by
rkakkar@uchicago.edu100 wrote:
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" >
probe affy annaffy • 357 views
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