[BioC] PLPE error

[Dennis.Burian at faa.gov]

Hello,
I'm using PLPE to compare six samples, two replicates.  I'm getting an
error that has me stumped.  I'm including the sessionInfo output and the
two input files I call for the function.

Also, if the developers could help me with the data.type argument to use
for Affy microarray data.  Thanks in advance,  DB

> sessionInfo()
R version 2.8.1 (2008-12-22)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] PLPE_1.2.0           MASS_7.2-45          LPE_1.16.0
 [4] affyQCReport_1.20.0  geneplotter_1.20.0   annotate_1.20.1
 [7] AnnotationDbi_1.4.2  lattice_0.17-20      RColorBrewer_1.0-2
[10] affyPLM_1.18.0       preprocessCore_1.4.0 xtable_1.5-4
[13] simpleaffy_2.18.0    gcrma_2.14.1         matchprobes_1.14.1
[16] genefilter_1.22.0    survival_2.34-1      affy_1.20.0
[19] Biobase_2.2.1

loaded via a namespace (and not attached):
[1] affyio_1.10.1      DBI_0.2-4          grid_2.8.1
KernSmooth_2.22-22
[5] RSQLite_0.7-1

> head(t1t2)
          t1_222.cel t1_224.cel t1_225.cel t1_226.cel t1_227.cel t1_233.cel
1007_s_at   5.813815   6.284673   6.086381   5.448039   5.588659   5.582803
1053_at     6.735783   5.387506   7.251909   7.389348   7.291360   6.978772
117_at      6.649979   7.202629   8.121696   9.646245   9.093114   9.511739
121_at      7.217766   7.191572   5.949533   6.221335   6.208934   6.316384
1255_g_at   4.000178   4.263894   3.451643   3.610458   3.627461   3.737950
1294_at     7.010166   6.650828   8.366195   8.359859   7.952251   8.382311
          t2_222.cel t2_224.cel t2_225.cel t2_226.cel t2_227.cel t2_233.cel
1007_s_at   5.553620   6.119633   6.800829   5.589128   5.596862   5.550595
1053_at     6.072061   6.116522   7.056313   7.024998   7.326683   7.361335
117_at      7.103895   5.828899   8.464786   9.453672   9.642708   9.330875
121_at      7.313019   6.855523   6.242273   6.177140   6.417202   6.183253
1255_g_at   4.043173   4.290510   3.708032   3.654016   3.636850   3.599941
1294_at     6.868946   6.611976   8.066763   7.861208   7.980915   8.202341
> design
      cond pair
 [1,]    1    1
 [2,]    1    2
 [3,]    1    3
 [4,]    1    4
 [5,]    1    5
 [6,]    1    6
 [7,]    2    1
 [8,]    2    2
 [9,]    2    3
[10,]    2    4
[11,]    2    5
[12,]    2    6
> t1t2out<-lpe.paired(x=t1t2,design=design,q=.01)
Error in lpe.paired.default(x = t1t2, design = design, q = 0.01) :
  element 2 is empty;
   the part of the args list of 'list' being evaluated was:
   (design = design, data.type = data.type, q = q, estimator = estimator,
w.estimator = w.estimator, w = w, test.out = data.out, iseed = iseed)
>