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Error to create a dds DESeq2 object.

Dear bioinformatic comunit,

I am new to using DESeq2, and I have a problem generating a dds object, in which I have the following error.

> dds.rsem <- DESeqDataSetFromTximport(tx.rsem, coldata, design = ~ Tissue + Location + Genotype + Time_point + Genotype:Time_point)
Error in validObject(.Object) :
  invalid class “SummarizedExperiment” object:
    nb of cols in 'assay' (1) must equal nb of rows in 'colData' (132)

However, when I look in my tx.rsem and coldata files look normal with the correct number of cols and rows, both with 132.

I would like to know if someone can give me some help, please?

I really appreciate any help you can provide.

deseq2 rnaseq
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written by cardon.chc • cardon.chc

No one can help you if they can't see a thing. Post the dimensions and first few lines of tx.rsem and coldata.

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written by swbarnes2 swbarnes2

Here are the first lines of coldata

                                                    Tissue Location  Genotype
ILWN_RNAseq_G002_ATCACG_Arachis_hypogaea_I801_L1      leaf        n     GTC20
ILWP_RNAseq_G026_TTAGGC_Arachis_hypogaea_I801_L1      leaf        n     GTC20
ILWQ_RNAseq_G050_ACTTGA_Arachis_hypogaea_I801_L1      leaf        n     GTC20
ILWR_RNAseq_T062_GATCAG_Arachis_hypogaea_I801_L1      leaf        n Tifrunner

first lines of tx.rsem:

  ILWN_RNAseq_G002_ATCACG_Arachis_hypogaea_I801_L1
arahy.Tifrunner.gnm1.ann1.0002EG                                             0.00
arahy.Tifrunner.gnm1.ann1.0003EL                                            13.53
arahy.Tifrunner.gnm1.ann1.0008XH                                             4.98
arahy.Tifrunner.gnm1.ann1.002YPW                                           339.12
arahy.Tifrunner.gnm1.ann1.0034KJ                                            15.75
arahy.Tifrunner.gnm1.ann1.0046K4                                             0.10
arahy.Tifrunner.gnm1.ann1.004CIH                                            19.30
arahy.Tifrunner.gnm1.ann1.004J0D                                            56.98
arahy.Tifrunner.gnm1.ann1.005C3Q                                             7.36
arahy.Tifrunner.gnm1.ann1.005S9P                                             0.0
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updated by GenoMax GenoMax • written by cardon.chc • cardon.chc

Okay...so are you absolutely positive that tx.rsem is in the right format for importing? It looks like your file has only a single column, and the error message suggests the same.

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written by swbarnes2 swbarnes2

Yes, I am.

Now I did not use some commands that I was using before and it worked. But I am not sure if it is correct, but all the next commands worked well.

I was using the following command which I am not using now.

colnames(tx.rsem$counts) <- sub("hypogaea","I801_L", colnames(tx.rsem$counts)) tx.rsem$counts <- tx.rsem$counts[rownames(coldata)]

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written by cardon.chc • cardon.chc

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