Hi,
I recently upgraded edgeR from 3.0.8 to 3.2.3 and I'm noticing some differences.  I have some data that I normalized with EDASeq.  I attempted to calculate the trended dispersion and I get the following error:

> dglmtrend=estimateGLMTrendedDisp(exprs(dataNormgcOff),design,offset=-offst(dataNormgcOff))

Error in t(y) + prior.count.scaled : non-conformable arrays

> class(dataNormgcOff)

[1] "SeqExpressionSet"

attr(,"package")

[1] "EDASeq"

> dim(exprs(dataNormgcOff))

[1] 19062    36

> dim(offst(dataNormgcOff))

[1] 19062    36

The error seems to occur in the aveLogCPM.default function due to matrix addition on two matrices with differing dimensions. Line 34 reads as:
abundance <- mglmOneGroup(t(t(y)+prior.count.scaled),dispersion=dispersion,offset=offset)

I no longer get an error if I change it to:
abundance <- mglmOneGroup(y+prior.count.scaled,dispersion=dispersion,offset=offset)

I don't think this is the best solution to fix all scenarios since I don't know this code very well.   So, I see some things have changed and I'm wondering if I need to make some changes in how I call the function or if there is really a bug of some kind here.

Thanks in advance for your help,
Suzy

> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] EDASeq_1.6.0         aroma.light_1.30.1   matrixStats_0.8.1    ShortRead_1.18.0
 [5] latticeExtra_0.6-24  RColorBrewer_1.0-5   Rsamtools_1.12.3     lattice_0.20-15
 [9] Biostrings_2.28.0    GenomicRanges_1.12.3 IRanges_1.18.1       Biobase_2.20.0
[13] BiocGenerics_0.6.0   edgeR_3.2.3          limma_3.16.3

loaded via a namespace (and not attached):
[1] annotate_1.38.0      AnnotationDbi_1.22.5 bitops_1.0-5         DBI_0.2-7
 [5] DESeq_1.12.0         genefilter_1.42.0    geneplotter_1.38.0   grid_3.0.0
 [9] hwriter_1.3          R.methodsS3_1.4.2    RSQLite_0.11.3       splines_3.0.0
[13] stats4_3.0.0         survival_2.37-4      tools_3.0.0          XML_3.96-1.1
[17] xtable_1.7-1         zlibbioc_1.6.0      _________________________________

Suzy Stiegelmeyer, PhD
Computational Biologist
Bioinformatics

Syngenta Biotechnology, Inc.
3054 Cornwallis Rd
Research Triangle Park, NC
27709
USA

phone +1 919 281 7472

suzy.stiegelmeyer@syngenta.com<mailto:suzy.stiegelmeyer@syngenta.com>
www.syngenta.com<http://www.syngenta.com/>




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