Question: results(dds) error: couldn't find results. you should first run DESeq()
gravatar for hs.lansdell
13 months ago by
hs.lansdell10 wrote:

Hello! After running DESeq, I attempted to see the results and the following is returned:

Error in results(dds) : 
  couldn't find results. you should first run DESeq()

This is right after successfully (I think) running DESeq. 

data<-read.csv("TotalRNA_reads.csv", header=TRUE, row.names = 1, stringsAsFactors = FALSE)
colnames(data) <- substring(colnames(data), 2)

colData<-read.csv("TotalRNA_Sample_Coldata.csv",header = TRUE, row.names = 1)
#Double check names match up between Sample and data matrix

dds<-DESeqDataSetFromMatrix(countData = data, colData = colData, design= ~condition)

keep <- rowSums(counts(dds)) >= 10
dds <- dds[keep,]  #keeps all but 89 genes 

The DESeq outputs this as it is running:

estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 11650 genes
-- DESeq argument 'minReplicatesForReplace' = 7 
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing
class: DESeqDataSet 
dim: 20451 192 
metadata(1): version
assays(5): counts mu cooks replaceCounts replaceCooks
rownames(20451): UBC|7316 GUCY2D|3000 ... LZTFL1|54585 CSF3|1440
rowData names(22): baseMean baseVar ... maxCooks replace
colnames(192): 649 1132 ... 11921 12010
colData names(4): condition type sizeFactor replaceable

So I believe it ran correctly... has anyone else encountered this issue with the results() function?


ADD COMMENTlink written 13 months ago by hs.lansdell10
gravatar for Gavin Kelly
13 months ago by
Gavin Kelly560
United Kingdom / London / Francis Crick Institute
Gavin Kelly560 wrote:

You've forgotten to assign the outputs of DESeq to anything; dds <- DESeq(dds) should sort things out for you

ADD COMMENTlink written 13 months ago by Gavin Kelly560

Wow. My bad. 

Thank you very much!

ADD REPLYlink modified 13 months ago • written 13 months ago by hs.lansdell10
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