[BioC] Globaltest

Jiuzhou song songjiuzhou at hotmail.com
Wed Feb 2 23:12:47 CET 2005


Hi, Fellows:

I want to try the globaltest package. The below are my data and phenotype, 
the try is 10*54000 gene expression data, phenotype is like a clinical data. 
When calling  globaltest, I got a error message said:Error: Y not among 
pData(X) variables. I don't know what's wrong. Enclosed is my organized data 
format:
>library(globaltest)
>library(hug133plus2)
>phenotype<-read.table("pdefnor.txt", header=TRUE)
>kegg<-as.list(hgu133plus2PATH2PROBE)
>cycle<-kegg[["04110"]]
>try[1:10, 1:10]
    1007_s_at  1053_at    117_at    121_at 1255_g_at  1294_at  1316_at
P01 1336.9781 979.6635  68.00548  942.4185 42.824334 240.2140 182.9987
P02 1244.8109 856.6623  17.18624  980.2785 61.589350 396.1784 156.9981
P03 1242.4112 892.5753  19.18659  917.2584  8.163818 293.9218 129.1083
P04 1514.9278 834.0531 104.18433  874.2615 42.987966 374.1156 126.5531
P05 1531.8062 561.8083 133.78595  721.0438 65.652205 235.9910 156.5618
P06 1244.6121 913.4974  86.32654 1204.2720 32.820671 182.1362 225.0419
P07 1030.4303 888.9043 168.81155  931.3331 60.896597 290.9441 124.4256
P08  967.8376 415.8462 140.10711 1054.7443 18.156250 250.7445 182.3890
P09  866.3241 368.4067 120.99928 1087.2129 41.717159 248.9227 199.6609
P10 1253.1630 941.2971 148.48320  968.1142 55.398853 261.7810 151.4873
      1320_at 1405_i_at   1431_at
P01 106.81913  3.123998 24.236890
P02  19.18795  8.798449 33.642152
P03  60.72386 24.951139 21.578197
P04  85.65980  2.569017  7.870907
P05 136.42790  3.486646 51.849258
P06  14.02785 10.497159 37.324950
P07  80.11405  8.150923 61.433460
P08  10.94902  3.646292 68.104859
P09  58.42698  8.727808 43.077735
P10  24.48091 23.979483 31.550727
>phenotype
    Phenotype
P01         0
P02         0
P03         0
P04         0
P05         0
P06         1
P07         1
P08         1
P09         1
P10         1
>gt.all<-globaltest(try,"phenotype")
Error: couldn't find function "globaltest"
>library(globaltest)
>gt.all<-globaltest(try,"phenotype")
Error: Y not among pData(X) variables
>globaltest(try, phenotype, cellcycle)
Error: Y not among pData(X) variables

is there anything wrong in my data? I greatly appreciate if any suggestion.

Thanks.

Yours

John



More information about the Bioconductor mailing list