In DESeqDataSet(se, design = design, ignoreRank)

[paulaberry]

The script is executing until about line 70, judging by the output files present (/Results/fold_changes/deltaTE.txt and Results/Results_figures.pdf, which is empty). I am getting an error that says:

In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted

I have reformatted my input files and tried the treatments with 1&2 and 0&1 and changed batches between 1&2 and 0&1 but get the same result.
ribo_counts.txt
rna_counts.txt
sample_info.txt

[soniachothani]

Hi Paula,

Your file formats look fine. I ran your data line by line to investigate the issue. First, tried to look at the PCA for the Ribo-seq data but I couldn't generate it because it seems most genes have 0 counts in Ribo-seq? May I check if this is a truncated file or is it the final count file?

length(which(rowSums(ribo) == 0))
[1] 17682
length(which(rowSums(ribo) != 0))
[1] 2742

If there is not enough depth in Ribo-seq - i.e. not enough genes with non-zero counts in Ribo or RNA, the result will be quite unreliable and in this case you find no DTEGs/DEGs, thus your result files are empty.

summary(res)
out of 11189 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up) : 0, 0%
LFC < 0 (down) : 0, 0%
outliers [1] : 0, 0%
low counts [2] : 0, 0%
(mean count < 0)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

Let me know.

Best,
Sonia