Hello, I am trying to normalize my ASVs across samples. I am running into an error with DESeqDataSetFromMatrix which indicates my variable names and column names are not matching When I investigate this I find that they are matching. Any ideas?

> head(sample_info_tab)
          Time Treatment Choice color
    D1S1     1         S      1   red
    D1S10    1         S      1   red
    D1S2     1         S      2   red
    D1S3     1         S      1   red
    D1S4     1         S      1   red
    D1S5     1         S      1   red

> head(count_tab)
      D1S1 D1S10 D1S2 D1S3 D1S4 D1S5 ...
ASV_1    0     0    0    0    0    0    0    0    0
ASV_2    0     0    0    0    0    0    0    0    0
ASV_3    0     0    0    0    0    0    0    0    0
ASV_4    0     0    0    0    0    0    0    0    0
ASV_5    0     0    0    0    0    0    0    0    0
ASV_6    0     0    0    0    0    0    0    0    0

> deseq_counts <- DESeqDataSetFromMatrix(countData = count_tab, colData = sample_info_tab, design = ~ treatment)
Error in DESeqDataSet(se, design = design, ignoreRank) :
  all variables in design formula must be columns in colData

However when I check that the names match there are no discrepancies

> c=colnames(count_tab)
> s=rownames(sample_info_tab)
> s==c

[1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

R version 3.6.1 (2019-07-05) Platform: x8664-condacos6-linux-gnu (64-bit) Running under: Ubuntu 19.10

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

other attached packages: [1] DESeq21.26.0 SummarizedExperiment1.16.1 DelayedArray0.12.2 BiocParallel1.20.1 [5] matrixStats0.56.0 Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 [9] IRanges2.20.2 S4Vectors0.24.3 BiocGenerics_0.32.0

treatment != Treatment

Note the error is

all variables in design formula must be columns in colData

Your columns in colData:

      Time Treatment Choice color

Your design formula:

design = ~ treatment

From: ericmalekos [bioc] noreply@bioconductor.org Sent: Thursday, April 16, 2020 3:34 PM To: Robert Thurman RThurman@seagen.com Subject: [EXTERNAL] [bioc] Error in DESeqDataSet: variables and colnames don't match when they do

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User ericmalekoshttps://support.bioconductor.org/u/23358/ wrote Question: Error in DESeqDataSet: variables and colnames don't match when they dohttps://support.bioconductor.org/p/130043/:

Hello, I am trying to normalize my ASVs across samples. I am running into an error with DESeqDataSetFromMatrix which indicates my variable names and column names are not matching When I investigate this I find that they are matching. Any ideas?

      Time Treatment Choice color

D1S1     1         S      1   red

D1S10    1         S      1   red

D1S2     1         S      2   red

D1S3     1         S      1   red

D1S4     1         S      1   red

D1S5     1         S      1   red

  D1S1 D1S10 D1S2 D1S3 D1S4 D1S5 ...

ASV_1 0 0 0 0 0 0 0 0 0

ASV_2 0 0 0 0 0 0 0 0 0

ASV_3 0 0 0 0 0 0 0 0 0

ASV_4 0 0 0 0 0 0 0 0 0

ASV_5 0 0 0 0 0 0 0 0 0

ASV_6 0 0 0 0 0 0 0 0 0

Error in DESeqDataSet(se, design = design, ignoreRank) :

all variables in design formula must be columns in colData

However when I check that the names match there are no discrepancies

[1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

R version 3.6.1 (2019-07-05) Platform: x8664-condacos6-linux-gnu (64-bit) Running under: Ubuntu 19.10

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

other attached packages: [1] DESeq21.26.0 SummarizedExperiment1.16.1 DelayedArray0.12.2 BiocParallel1.20.1 [5] matrixStats0.56.0 Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 [9] IRanges2.20.2 S4Vectors0.24.3 BiocGenerics_0.32.0