Hello,

I am having the hardest time determining what in my original file is misaligned and why this error message persists. Any suggestions? I added the columns "status" and "sample" and those are the only columns that align with the data. I am not sure what is missing .

 #Import data
> getwd()

> samples <- read.table("data/samples_updated.txt", header = TRUE)

> samples

    sample status
1    10007 urgent
2    10018  asymp
3    10037 urgent
4    10045 urgent
5    10047  asymp
6    10049 urgent
7  011811A  asymp
8  051111A  asymp
9  051512A urgent
10 111111A  asymp
11 121511A urgent

> dir <- "data"

> files <- file.path(dir, paste0(samples$sample, ".genes.results"))

> names(files) <- paste0("sample", 1:11)

> all(file.exists(files))
[1] TRUE

> txi.rsem <- tximport(files, type = "rsem", txIn = FALSE, txOut = FALSE)
reading in files with read_tsv
1 2 3 4 5 6 7 8 9 10 11 

> head(txi.rsem$counts)
          sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9 sample10 sample11
5S_rRNA      0.00    0.00    1.51    0.00    0.00    2.94    1.00    1.00    0.79     1.16     0.00
5_8S_rRNA    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00     0.00     0.00
7SK         60.28   47.00   67.30   33.94   62.29   42.90   78.67   60.04   84.67    56.25   107.75
A1BG        78.08   40.82   75.10   75.24   68.61   53.74   69.94   43.81   61.44    60.16    54.27
A1BG-AS1    90.00   57.00  112.57   93.03   78.98   65.00   72.00   74.00   78.98    32.38    97.00
A1CF         4.10    0.00    2.04    3.11    5.13    1.47    1.41    4.27    3.20     3.68     8.00
> 

> #import into DESeq2

> sampleTable <- data.frame(read.csv("data/samples_updated.txt", header=T))

> rownames(sampleTable) <- colnames(txi.rsem$counts)

> txi.rsem$length <- replace (txi.rsem$length, txi.rsem$length==0,1)

*> dds <- DESeqDataSetFromTximport(txi.rsem, sampleTable, ~Status)
Error in DESeqDataSet(se, design = design, ignoreRank) : 
  all variables in design formula must be columns in colData*