Re-analysis of a dataset which strange differential expressed genes

deseq_zero_counts.Rmd

```{r }
library("recount3")
library("data.table")
library("magrittr")
library("DESeq2")

rse <- recount3::create_rse_manual(
    project = "ERP010060",
    project_home = "data_sources/sra",
    organism = "human",
    annotation = "gencode_v26",
    type = "gene"
)

sample_info <- colData(rse) %>%
    as.data.frame() %>%
    setDT(keep.rownames="sample_id") %>% 
    .[, c("sample_id", "sra.experiment_attributes", "sra.sample_title")] %>% 
    .[, siRNA := gsub("Experimental Factor: RNA interference;;(.+)\\|Experimental Factor: stimulus;;(.+)\\|LIBRARY_STRAND;;first strand", "\\1", sra.experiment_attributes)] %>% 
    .[, siRNA := gsub(" antisense oligonucleotide", "", siRNA)] %>% 
    .[, stimulus := gsub("Experimental Factor: RNA interference;;(.+)\\|Experimental Factor: stimulus;;(.+)\\|LIBRARY_STRAND;;first strand", "\\2", sra.experiment_attributes)] %>%  
    .[, replicate := gsub(".+:Sample (\\d)", "\\1", sra.sample_title)] %>%
    .[, replicate := ifelse(replicate == "", sample(.$replicate[!is.na(.$replicate)], 1), replicate)] %>%
    .[, siRNA_stimulus := paste(siRNA, stimulus, sep = "_")] %>%
    .[, c("sample_id", "siRNA", "stimulus", "replicate", "siRNA_stimulus")] %>%
  as.data.frame()
rownames(sample_info) <- sample_info$sample_id

cnts <- assay(rse, "raw_counts") %>% 
    as.data.frame() %>%
    setDT(keep.rownames="gene_id") %>%
   .[ !like(gene_id, "_PAR_Y")] %>%
   .[, gene_id := gsub("\\.\\w+$", "", gene_id)] %>%
   as.matrix(rownames = "gene_id") 

```

```{r }
dds <- DESeqDataSetFromMatrix(
	countData=cnts,
	colData=sample_info,
	design=~siRNA_stimulus
)

```



```{r }
dds <- DESeq(dds)
res <- results(dds, name = "siRNA_stimulus_scrambled_KCl_vs_NEAT1_KCl")
res

```

plot 1

plot 2

plot 3