hello,

i am testing the change of miRNA expression between 2 time periods in a set of matched patient samples (100 ‘before', 100 ‘after’).
after filtering very low coverage miRNA i am left with ~500 miRNA

i then define:

countData <- as.matrix(round(raw_reads))  # raw_reads is the dataframe of miRNA counts (rows) by sample (columns)
colData <- data.frame (patient, period)   # period is a ‘before' and ‘after’ factor; patient is 1:100

ddsE <- DESeqDataSetFromMatrix(countData = countData,
colData = colData,
design = ~ period+patient)

ddsE<-DESeq(ddsE)

the following messages appear:

> ddsE<-DESeq(ddsE)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
Error in simpleLoess(y, x, w, span, degree, parametric, drop.square, normalize,  :
  NA/NaN/Inf in foreign function call (arg 1)

this error does not occur if i further diminish my gene list by filtering additional low coverage genes.

can anyone suggest a solution that will allow me to test all the miRNA of interrest using DESeq2?

thanks,
iddo

> traceback()
8: simpleLoess(y, x, w, span, degree, parametric, drop.square, normalize,
       control$statistics, control$surface, control$cell, iterations,
       control$trace.hat)
7: loess(lpo ~ s, span = 0.1)
6: fitDispInR(y = counts(objectNZ)[refitDisp, , drop = FALSE], x = modelMatrix,
       mu = mu[refitDisp, , drop = FALSE], logAlphaPriorMean = rep(0,
           sum(refitDisp)), logAlphaPriorSigmaSq = 1, usePrior = FALSE)
5: estimateDispersionsGeneEst(object, maxit = maxit, quiet = quiet)
4: .local(object, ...)
3: estimateDispersions(object, fitType = fitType, quiet = quiet)
2: estimateDispersions(object, fitType = fitType, quiet = quiet)
1: DESeq(ddsE)

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] ggplot2_1.0.0             RColorBrewer_1.0-5        gplots_2.14.2             ReportingTools_2.4.0     
 [5] AnnotationDbi_1.26.1      Biobase_2.24.0            RSQLite_0.11.4            DBI_0.3.1                
 [9] knitr_1.6                 DESeq2_1.4.5              RcppArmadillo_0.4.450.1.0 Rcpp_0.11.3              
[13] GenomicRanges_1.16.4      GenomeInfoDb_1.0.2        IRanges_1.22.10           BiocGenerics_0.10.0      
[17] plyr_1.8.1                genefilter_1.46.1         matrixStats_0.10.0        pheatmap_0.7.7           
[21] scatterplot3d_0.3-35      edgeR_3.6.8               limma_3.20.9             

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3          annotate_1.42.1          AnnotationForge_1.6.1    base64enc_0.1-2         
 [5] BatchJobs_1.4            BBmisc_1.7               BiocParallel_0.6.1       biomaRt_2.20.0          
 [9] Biostrings_2.32.1        biovizBase_1.12.3        bitops_1.0-6             brew_1.0-6              
[13] BSgenome_1.32.0          Category_2.30.0          caTools_1.17.1           checkmate_1.4           
[17] cluster_1.15.3           codetools_0.2-9          colorspace_1.2-4         dichromat_2.0-0         
[21] digest_0.6.4             evaluate_0.5.5           fail_1.2                 foreach_1.4.2           
[25] foreign_0.8-61           formatR_1.0              Formula_1.1-2            gdata_2.13.3            
[29] geneplotter_1.42.0       GenomicAlignments_1.0.6  GenomicFeatures_1.16.3   ggbio_1.12.10           
[33] GO.db_2.14.0             GOstats_2.30.0           graph_1.42.0             grid_3.1.1              
[37] gridExtra_0.9.1          GSEABase_1.26.0          gtable_0.1.2             gtools_3.4.1            
[41] Hmisc_3.14-5             hwriter_1.3.2            iterators_1.0.7          KernSmooth_2.23-13      
[45] labeling_0.3             lattice_0.20-29          latticeExtra_0.6-26      locfit_1.5-9.1          
[49] MASS_7.3-35              Matrix_1.1-4             munsell_0.4.2            nnet_7.3-8              
[53] PFAM.db_2.14.0           proto_0.3-10             R.methodsS3_1.6.1        R.oo_1.18.0             
[57] R.utils_1.34.0           RBGL_1.40.1              RCurl_1.95-4.3           reshape2_1.4            
[61] rpart_4.1-8              Rsamtools_1.16.1         rtracklayer_1.24.2       scales_0.2.4            
[65] sendmailR_1.2-1          splines_3.1.1            stats4_3.1.1             stringr_0.6.2           
[69] survival_2.37-7          tools_3.1.1              VariantAnnotation_1.10.5 XML_3.98-1.1            
[73] xtable_1.7-4             XVector_0.4.0            zlibbioc_1.10.0