[R] ERROR with Aggregate differentially expressed genes across all contrast results using DEVis/DESeq

[Jim Lemon]

Hi Ana,
I don't have your data or the package you are using, but the "NULL
object" error associated with "names" may mean that there are no
"rownames" in one of your inputs. That is, if you ask:

names(myobject)
NULL

if myobject has no names. I would look carefully at the example for
the function you are using to see if your object has all the required
names.

Jim

On Thu, Jun 30, 2022 at 4:55 AM Ana Ruiz Manzano <aruizman2 using gmail.com> wrote:
>
> 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 RStudio 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!
>
>
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