Hello

1) I have two imput files: countData (counts of reads per gene, RNAseq type of data) and colData as .csv.

> colData<-read.csv("Pine_ColData.csv", sep=";", header=TRUE, check.names=FALSE,row.names=1)
> countData<-read.csv("Pine_RNAseq_no outliers.csv", sep=";", header=TRUE, check.names=FALSE, row.names=1)> 

2) I created the dds<-DESeqDataSetFromMatrix

> dds<-DESeqDataSetFromMatrix(countData=countData,colData=colData,design=~TREAT+LAT)
> head(dds)
class: DESeqDataSet
dim: 6 16
metadata(0):
assays(1): counts
rownames(6): 1A_I11_NT_comp41909_c0_seq1|m.4335.path1.0 1A_I11_NT_comp41909_c0_seq1|m.4335.path2.0 ...
  1A_I11_NT_comp45669_c0_seq3|m.4374.path2.0 1A_I11_NT_comp46081_c0_seq2|m.4378.path1.0
rowRanges metadata column names(0):
colnames(16): A-P56-1 A-P56-3 ... B-P67-4 D-P56-4
colData names(2): TREAT LAT

3) when I try to run DEseq(dds) I got this error;

estimating size factors
estimating dispersions
gene-wise dispersion estimates
Error in model.matrix.formula(design(object), data = colData(object)) :
  data must be a data.frame

4) I checked with is.data.frame(colData) and it returns [TRUE].

is.data.frame(colData)
[1] TRUE
> is.data.frame(countData)
[1] TRUE

5) In that case, what is the problem?

I appreciate your help. (I could send you the original csv files if you want)

Maria

Can you show colData? Also what is your sessionInfo()

Update [8/7/2016] I've updated the code in DESeq2 v1.12.4 which should fix this conflict:

> packageVersion("DESeq2")
[1] ‘1.12.4’

Hello

colData

Sorry, I am not familiar with sessionInfo(), I checked and it is a function under package Utils. What exactly are you after? The input files, or the functions that I am using?

Regards

Maria

Here

> sessionInfo()

R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

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] stats4    parallel  grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DESeq_1.22.1               lattice_0.20-33            locfit_1.5-9.1             pasilla_0.10.0            
 [5] DESeq2_1.10.1              RcppArmadillo_0.6.600.4.0  Rcpp_0.12.3                airway_0.104.0            
 [9] SummarizedExperiment_1.0.2 Biobase_2.30.0             GenomicRanges_1.22.4       GenomeInfoDb_1.6.3        
[13] IRanges_2.4.8              S4Vectors_0.8.11           BiocGenerics_0.16.1        BiocInstaller_1.20.1      
[17] glm2_1.1.2                 lme4_1.1-11                Matrix_1.2-4               agricolae_1.2-3           
[21] ggbiplot_0.55              scales_0.4.0               plyr_1.8.3                 ggplot2_2.1.0             
[25] devtools_1.10.0            gridExtra_2.2.1           

loaded via a namespace (and not attached):
 [1] deldir_0.1-12        digest_0.6.9         R6_2.1.2             AlgDesign_1.1-7.3    futile.options_1.0.0
 [6] acepack_1.3-3.3      RSQLite_1.0.0        coda_0.18-1          httr_1.1.0           zlibbioc_1.16.0     
[11] spdep_0.5-92         curl_0.9.6           minqa_1.2.4          annotate_1.48.0      nloptr_1.0.4        
[16] rpart_4.1-10         combinat_0.0-8       labeling_0.3         splines_3.2.3        BiocParallel_1.4.3  
[21] geneplotter_1.48.0   foreign_0.8-66       munsell_0.4.3        nnet_7.3-12          Hmisc_3.17-2        
[26] XML_3.98-1.4         MASS_7.3-45          nlme_3.1-126         xtable_1.8-2         gtable_0.2.0        
[31] DBI_0.3.1            git2r_0.14.0         XVector_0.10.0       genefilter_1.52.1    LearnBayes_2.15     
[36] sp_1.2-2             latticeExtra_0.6-28  futile.logger_1.4.1  boot_1.3-18          Formula_1.2-1       
[41] klaR_0.6-12          lambda.r_1.1.7       RColorBrewer_1.1-2   tools_3.2.3          survival_2.38-3     
[46] AnnotationDbi_1.32.3 colorspace_1.2-6     cluster_2.0.3        memoise_1.0.0       

Hi,

Was this resolved?  I have a similar problem.

Thanks.

Two random suggestions

- "colData" is the name of the Bioconductor function used to access the column data of a SummerizedExperiment object (and hence also of a DESeqDataSet). As you named your sample data the same, you may have accidentally overwritten the function, and so caused random errors. (This shouldn't happen because R keeps variable and function names separate, but who knows.)

Just try again, using another name than "colData".

- Why do you have only 6 rows? Maybe something is wrong there, too. If you really have only 16 genes, DESeq2 might not be the right tool for the job.

I faced a similar problem, but restarting r-season helped. seems some variables from other scripts were interfering