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Dennis.Burian@faa.gov
▴
90
@dennisburianfaagov-2126
Last seen 7.5 years ago
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_N
AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI
FICATION=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)
>