[DESeq2] Little Error in seq_len(nrow(modelMatrix)) while starting DESeq()

Question

[john]

Hello guys,

I am doing some RNA-seq analysis with DESeq2. The following error occurs (I sure it's me causing it). Pls help me out!

Warning messages:
2: In seq_len(nrow(modelMatrix)) :
  first element used of 'length.out' argument
Error in sapply(seq_len(nrow(modelMatrix)), function(i) { :
  error in evaluating the argument 'X' in selecting a method for function 'sapply': Error in seq_len(nrow(modelMatrix)) :
  argument must be coercible to non-negative integer

This is what I did so far:

>ddsfm <- DESeqDataSetFromMatrix(countData = countdata, colData = coldata, design = ~ time)
> head(assay(ddsfm))
         h0_1 h2_2 h4_3 h6_4 h8_5 h10_6 h12_7 h14_8 h24_9 h48_10
A1BG-AS1   17   12   19   47   28     4    12    36    31    114
A1CF        0    1    2    2    4     0     0     5     3     22
A2M         3    4    6   18   11    20    20    18    17     60
A2M-AS1     0    3    1    6    0    10     4     9     2     12
A2ML1       0    0    3    4    6     2     2     2     3      7
A2MP1       9   20   34  144   97     5    35    72    69    112

> coldata
       intercept time
h0_1           1   h0
h2_2           1   h2
h4_3           1   h4
h6_4           1   h6
h8_5           1   h8
h10_6          1  h10
h12_7          1  h12
h14_8          1  h14
h24_9          1  h24
h48_10         1  h48

>dds=DESeq(ddsfm,test="LTR",reduced= ~ 1, fitType='local')

----------------
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

Warning messages:
2: In seq_len(nrow(modelMatrix)) :
  first element used of 'length.out' argument
Error in sapply(seq_len(nrow(modelMatrix)), function(i) { :
  error in evaluating the argument 'X' in selecting a method for function 'sapply': Error in seq_len(nrow(modelMatrix)) :
  argument must be coercible to non-negative integer

I don't really know where I made a mistake.

Any help is greatly appreciated!

Cheers

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: i686-pc-linux-gnu (32-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] DESeq2_1.6.3              RcppArmadillo_0.4.600.4.0
[3] Rcpp_0.11.4               GenomicRanges_1.18.4
[5] GenomeInfoDb_1.2.4        IRanges_2.0.1
[7] S4Vectors_0.4.0           BiocGenerics_0.12.1

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3      annotate_1.44.0      AnnotationDbi_1.28.1
 [4] base64enc_0.1-2      BatchJobs_1.5        BBmisc_1.9
 [7] Biobase_2.26.0       BiocParallel_1.0.3   brew_1.0-6
[10] checkmate_1.5.1      cluster_2.0.1        codetools_0.2-10
[13] colorspace_1.2-4     DBI_0.3.1            digest_0.6.8
[16] fail_1.2             foreach_1.4.2        foreign_0.8-62
[19] Formula_1.2-0        genefilter_1.48.1    geneplotter_1.44.0
[22] ggplot2_1.0.0        grid_3.1.1           gtable_0.1.2
[25] Hmisc_3.14-6         iterators_1.0.7      lattice_0.20-29
[28] latticeExtra_0.6-26  locfit_1.5-9.1       MASS_7.3-37
[31] munsell_0.4.2        nnet_7.3-9           plyr_1.8.1
[34] proto_0.3-10         RColorBrewer_1.1-2   reshape2_1.4.1
[37] rpart_4.1-9          RSQLite_1.0.0        scales_0.2.4
[40] sendmailR_1.2-1      splines_3.1.1        stringr_0.6.2
[43] survival_2.37-7      tools_3.1.1          XML_3.98-1.1
[46] xtable_1.7-4         XVector_0.6.0

Answer 1

[Michael Love]

it should be test="LRT"

I do have match.arg checks now for test but not before version 1.6 went out. In the next release it will give a nicer message :)

[john]

What is it that these little mistakes always get me? :-D

Thanks Michael!