[BioC] Globaltest

[Oosting, J. (PATH)]

Hi,

You can only get this message when the first argument (try) is an exprSet object, but in exprSets the columns are the samplenames, and the rows have the genenames. This is not the case in your example. 
+ The error only occurs when the length of the second argument is 1, your second call (globaltest(try, phenotype, cellcycle)) should not cause this error because phenotype has length 10 there. The first call could work if you assign phenotype to the phenodata attribute of the exprSet object.

try is an unfortunate variable name because it is also a standard function in R

if try is an exprSet the output after try[1:10,1:10] does not fit, it should be something like:
Expression Set (exprSet) with 
        10 genes
        10 samples
                 phenoData object with 3 variables and 10 cases
         varLabels
 
So:
- Something is definitely not right in your data, and I think you're not giving a complete log af a session (note: also difference in cycle and cellcycle names of pathway variable)

please state the version number of globaltest you're using if you have further questions.

With kind regards,

Jan






> 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
> 
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