[BioC] ComBat crash/problem

[Peter Langfelder]

Dear Evan,

I encountered what seems to be a bug in ComBat. Running the following code

cb = ComBat(data.problem, batch = batch.problem, mod =
model.matrix(~1, data = data.frame(batch.problem)))

using data contained in the attached RData file (I assume the RData
file will get stripped out of Bioconductor but you should receive it
directly), I get the following output:

Found 2 batches
Found 0  categorical covariate(s)
Standardizing Data across genes
Fitting L/S model and finding priors
Finding parametric adjustments
Error in while (change > conv) { : missing value where TRUE/FALSE needed

Looking at the source code it seems the problem happens in the it.sol
function where in the very first iteration the entire g.new is filled
with missing data, causing change to be NA, which generates the
problem in the second iteration.

Neither the input data nor the batch variable contain any missing entries.

This happens with sva_3.10.0 downloaded freshly from bioconductor.org.

Thanks for your help,

Peter

> sessionInfo()
R version 3.0.2 Patched (2013-10-08 r64039)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
LC_PAPER=en_US.utf8       LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] org.Mm.eg.db_2.10.1     DESeq2_1.2.10
RcppArmadillo_0.4.200.0 Rcpp_0.11.1
 [5] GenomicRanges_1.14.4    XVector_0.2.0           IRanges_1.20.7
      JamsPlenTFun_0.70
 [9] GO.db_2.10.1            AnnotationDbi_1.24.0    Biobase_2.22.0
      BiocGenerics_0.8.0
[13] WGCNA_1.40              flashClust_1.01-2
dynamicTreeCut_1.62     preprocessCore_1.24.0
[17] sqldf_0.4-7.1           RSQLite.extfuns_0.0.1   RSQLite_0.11.4
      DBI_0.2-7
[21] gsubfn_0.6-5            proto_0.3-10
matrixStats_0.8.14      doParallel_1.0.8
[25] iterators_1.0.6         foreach_1.4.1           reshape_0.8.4
      plyr_1.8.1
[29] Hmisc_3.14-3            Formula_1.1-1           survival_2.37-7
      lattice_0.20-29
[33] impute_1.36.0           cluster_1.15.2          class_7.3-10
      MASS_7.3-31
[37] sva_3.10.0              mgcv_1.7-29             nlme_3.1-117
      corpcor_1.6.6

loaded via a namespace (and not attached):
 [1] annotate_1.40.1     chron_2.3-45        codetools_0.2-8
genefilter_1.44.0   latticeExtra_0.6-26
 [6] locfit_1.5-9.1      Matrix_1.1-3        R.methodsS3_1.6.1
RColorBrewer_1.0-5  stats4_3.0.2
[11] XML_3.98-1.1        xtable_1.7-3