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

[Ana Ruiz Manzano]

Thanks for replying! And sorry for the formatting, I actually read about it
but sent the email before realizing.

I previously posted this in the Bioconductor forum but then sent me to you.

Ana

On Wed, Jun 29, 2022 at 14:08 Jeff Newmiller <jdnewmil using dcn.davis.ca.us>
wrote:

> This question should most likely have been asked in the Bioconductor
> support forum.
>
> For future reference, if you are looking for help with R rather than deep
> details about using a non-CRAN package, do turn off HTML formatting in your
> email software when you send to this list, as such formatting gets stripped
> anyway and what is left is barely legible.
>
> On June 29, 2022 9:05:11 AM PDT, 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!
> >
> >
> >       [[alternative HTML version deleted]]
> >
>
> --
> Sent from my phone. Please excuse my brevity.
>

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