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Jiuzhou song
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100
@jiuzhou-song-1051
Last seen 10.2 years ago
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