can not obtain DESeq2 results

Question

[zehrahazalsezer]

Hi Everyone,

For differential expression analysis with DESeq package, i encountered problems with obtaining DESeq results. You can find my partial scripts below.

dds <- DESeqDataSetFromTximport(txi.salmon, colData = colData, ~condition)

it gives dds file as a Large DESeq Dataset and it contains 35721 elements. But when i want to see result like this code:

result_ctrl_vs_casin = results(dds, contrast=c("condition", "control","not_control_casin"), cooksCutoff=FALSE, independentFiltering=FALSE)

And it gives errors:

Error in results(dds, contrast = c("condition", "control", "not_control_casin"),  : 
  couldn't find results. you should first run DESeq()

Thank you for helping, i am looking forward to hearing from you.

[Bastien Hervé]

Did you run this : dds <- DESeq(dds) ?

[zehrahazalsezer]

Thanks for answer, it solves my problems!

[zehrahazalsezer]

i also used DESeq() function but it gave same errors.

[Devon Ryan]

Then you should start with that as a question and provide the error message.

Answer 1

[Santosh Anand]

The answer is right in front of you:

couldn't find results. you should first run DESeq()

You haven't run the DESeq() function yet, which is needed to create the result.

Please follow DESeq2 tutorial https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html