Hi to everybody,

I hope someone can help me on this as I am losing my health.

I was re running my script today which worked fine till last time I did it. When I run the topTable function on more than one coefficient it gives me the following error.

> x.contrast.REG <- topTable(fit.contrast, adjust.method="none", coef=c(1:4), number=20000, p.value = 0.05)
Error in `row.names<-.data.frame`(`*tmp*`, value = value) :
  duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names':

I have tried to run the same script for each coefficient separately and it works fine. I can't explain the error since if there were duplicated row.names then I should get the same error when doing the analysis on individual contrasts since I run topTable on the fit object.

The only thing I have changed was the fact that this morning I updated Bioconductor to the latest release.

I really hope someone can help me understand.

Regards,
Christian De Santis

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252

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

other attached packages:
[1] reshape2_1.2.2       ellipse_0.3-8        genefilter_1.44.0    limma_3.18.1         BiocInstaller_1.12.0

loaded via a namespace (and not attached):
 [1] annotate_1.40.0      AnnotationDbi_1.24.0 Biobase_2.22.0       BiocGenerics_0.8.0   DBI_0.2-7
 [6] IRanges_1.20.3       parallel_3.0.1       plyr_1.8             RSQLite_0.11.4       splines_3.0.1
[11] stats4_3.0.1         stringr_0.6.2        survival_2.37-4      tools_3.0.1          XML_3.98-1.1
[16] xtable_1.7-1




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