Aggregate differentially expressed genes across all contrast results using DEVis

[aruizman]

Hi,

I'm using DEVis for differential expression analysis. When I get to running DESeq I get an error about "object of class “NULL” is not valid" when I'm creating the aggregated data.

running BiocManager::valid() returns [1] TRUE and restarting RStudion didn't solve it either.

#Run DESeq on my previously prepared DESeq2 object. 
    dds <- DESeq(dds) 

#determine the contrasts we are interested in examining by using DESeq2's results() function
    res.SAMPLE3.vs.C2 <- results(dds, contrast=c("condition_ppGpp", "untreated_0mM", "treated_0.5mM")) 
    res.SAMPLE4.vs.C2 <- results(dds, contrast=c("condition_ppGpp", "untreated_0mM", "treated_1mM"))
    print(res.SAMPLE3.vs.C2)
log2 fold change (MLE): condition_ppGpp untreated_0mM vs treated_0.5mM 
Wald test p-value: condition ppGpp untreated 0mM vs treated 0.5mM 
DataFrame with 3996 rows and 6 columns
      baseMean log2FoldChange     lfcSE       stat    pvalue      padj
     <numeric>      <numeric> <numeric>  <numeric> <numeric> <numeric>
1      352.326      0.2830664  0.391703  0.7226560 0.4698913 0.6771991
2      335.373      0.5624211  0.270855  2.0764617 0.0378513 0.1542207
3      315.891      0.6081361  0.237291  2.5628297 0.0103823 0.0653239
4      326.854     -0.0200133  0.275640 -0.0726069 0.9421189 0.9702167
5      360.061     -0.6693134  0.317713 -2.1066623 0.0351469 0.1471803
...        ...            ...       ...        ...       ...       ...
3992 0.1194548       -3.02243   4.02648  -0.750639   0.45287        NA
3993 0.0481303        0.00000   4.06264   0.000000   1.00000        NA
3994 0.0481303        0.00000   4.06264   0.000000   1.00000        NA
3995 0.0481303        0.00000   4.06264   0.000000   1.00000        NA
3996 0.1218624        0.00000   4.06264   0.000000   1.00000        NA

#Make a list of all of our contrasts.
    result_list <- list(res.SAMPLE3.vs.C2, res.SAMPLE4.vs.C2)
    print(result_list)

#Aggregate differentially expressed genes across all contrast results.
    master_dataframe <- create_master_res(result_list, filename="master_DE_list.txt", method="union", lfc_filter=TRUE)

Error in (function (cl, name, valueClass)  : 
  assignment of an object of class “NULL” is not valid for @‘allNames’ in an object of class “DESeqResMeta”; is(value, "character") is not TRUE

I have tried to replace the NA data points in my data to zeros using the is.na() <- 0 function, but then I get an error

Error in create_master_res(result_list, filename = "master_DE_list.txt",  : 
  create_master_res() requires list type object containing DESeq result sets.

Changing data.frame to list didn't hep either.

What I am missing?

Thanks!