Ana Ruiz Manzano
2022-Jun-29 16:05 UTC
[R] ERROR with Aggregate differentially expressed genes across all contrast results using DEVis/DESeq
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]]
Jeff Newmiller
2022-Jun-29 19:08 UTC
[R] ERROR with Aggregate differentially expressed genes across all contrast results using DEVis/DESeq
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 at 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.
Jim Lemon
2022-Jun-29 19:43 UTC
[R] ERROR with Aggregate differentially expressed genes across all contrast results using DEVis/DESeq
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 at 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]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.