I am currently getting an error when I try to calculate robust fpkm values using DESeq2 with Kallisto transcript data imported with tximport. I am assuming it is because sizeFactors(object) is NULL after calling estimateSizeFactors(object) in the fpm() method.

library(tximport)
library(DESeq2)
library(readr)

> txi <- tximport(files, type="kallisto", tx2gene=tx2gene, ignoreTxVersion=TRUE, reader=read_tsv)

reading in files
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 summarizing abundance
summarizing counts
summarizing length

> dds <- DESeqDataSetFromTximport(txi, colData=samples, design=~0 + fraction)
using counts and average transcript lengths from tximport

> dds <- DESeq(dds, betaPrior=FALSE)
estimating size factors
using 'avgTxLength' from assays(dds), correcting for library size
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

> f <- fpkm(dds)
using 'avgTxLength' from assays(dds), correcting for library size
Warning message:
In max(cumDim[cumDim <= lstats]) :
  no non-missing arguments to max; returning -Inf

Session Info:

R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.4 (El Capitan)

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  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] readr_0.2.2                DESeq2_1.12.0              SummarizedExperiment_1.2.0 Biobase_2.32.0             GenomicRanges_1.24.0      
 [6] GenomeInfoDb_1.8.0         IRanges_2.6.0              S4Vectors_0.10.0           BiocGenerics_0.18.0        tximport_1.0.0            

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.4.5        RColorBrewer_1.1-2   plyr_1.8.3           XVector_0.12.0       zlibbioc_1.18.0      rpart_4.1-10         RSQLite_1.0.0       
 [8] annotate_1.50.0      gtable_0.2.0         lattice_0.20-33      Matrix_1.2-6         DBI_0.4              gridExtra_2.2.1      genefilter_1.54.0   
[15] cluster_2.0.4        locfit_1.5-9.1       grid_3.3.0           nnet_7.3-12          data.table_1.9.6     AnnotationDbi_1.34.0 XML_3.98-1.4        
[22] survival_2.39-2      BiocParallel_1.6.0   foreign_0.8-66       latticeExtra_0.6-28  Formula_1.2-1        geneplotter_1.50.0   ggplot2_2.1.0       
[29] Hmisc_3.17-4         scales_0.4.0         splines_3.3.0        colorspace_1.2-6     xtable_1.8-2         acepack_1.3-3.3      munsell_0.4.3       
[36] chron_2.3-47        

hi,

Thanks for the bug report. I'll have to work on this in the devel branch and then eventually put a fix through to release. In the meantime you can do:

f <- fpkm(dds, robust=FALSE)
sf <- estimateSizeFactorsForMatrix(f)
f2 <- t(t(f)/sf)

This just applies the DESeq normalization method ("median ratio") to the standard FPKM matrix.