invalid class “MetaVolcano” object: || Rv 4.0 and MetaVolcanoR 1.2.0

[complexgenome]

Hi there,

I'm interested to use metavolcano for analysis two datasets. I've list with length two. The column names are "Symbol" "Log2FC" "CI.L" "CI.R" "pvalue"
Symbol column is of class character, rest are numeric.

sapply(dge_list[[2]],class)
     Symbol      Log2FC        CI.L        CI.R      pvalue
"character"   "numeric"   "numeric"   "numeric"   "numeric"

I run into error when I run combined approach of invalid class as the following command:

meta_degs_comb <- combining_mv(diffexp=dge_list, pcriteria='pvalue',
 foldchangecol='Log2FC', genenamecol='Symbol',geneidcol=NULL,metafc='Mean',
metathr=0.05,collaps=TRUE, 
 jobname="MetaVolcano",outputfolder=".",    draw='HTML')

Error in validObject(.Object) :
invalid class “MetaVolcano” object: invalid object for slot "inputnames" in class "MetaVolcano": got class "NULL", should be or extend class "character"
In addition: There were 50 or more warnings (use warnings() to see the first 50)

Below is the sessioninfo:

R version 4.0.0 (2020-04-24)
other attached packages:
[1] MetaVolcanoR_1.2.0

loaded via a namespace (and not attached):
 [1] zoo_1.8-8           tidyselect_1.1.0    purrr_0.3.4
 [4] TFisher_0.2.0       splines_4.0.0       lattice_0.20-41
 [7] colorspace_1.4-1    vctrs_0.3.1         generics_0.0.2
[10] htmltools_0.5.0     stats4_4.0.0        viridisLite_0.3.0
[13] yaml_2.2.1          survival_3.1-12     plotly_4.9.2.1
[16] rlang_0.4.6         pillar_1.4.4        sn_1.6-2
[19] glue_1.4.1          metap_1.3           BiocGenerics_0.34.0
[22] multcomp_1.4-13     lifecycle_0.2.0     stringr_1.4.0
[25] munsell_0.5.0       gtable_0.3.0        htmlwidgets_1.5.1
[28] mvtnorm_1.1-1       codetools_0.2-16    labeling_0.3
[31] Biobase_2.48.0      crosstalk_1.1.0.1   Cairo_1.5-12.2
[34] mutoss_0.1-12       gbRd_0.4-11         parallel_4.0.0
[37] TH.data_1.0-10      Rcpp_1.0.4.6        scales_1.1.1
[40] BiocManager_1.30.10 plotrix_3.7-8       jsonlite_1.6.1
[43] tmvnsim_1.0-2       topconfects_1.4.0   farver_2.0.3
[46] mnormt_2.0.1        ggplot2_3.3.2       digest_0.6.25
[49] stringi_1.4.6       dplyr_1.0.0         numDeriv_2016.8-1.1
[52] cowplot_1.0.0       grid_4.0.0          bibtex_0.4.2.2
[55] Rdpack_1.0.0        tools_4.0.0         sandwich_2.5-1
[58] magrittr_1.5        lazyeval_0.2.2      tibble_3.0.1
[61] crayon_1.3.4        tidyr_1.1.0         pkgconfig_2.0.3
[64] ellipsis_0.3.1      MASS_7.3-51.6       Matrix_1.2-18
[67] data.table_1.12.8   assertthat_0.2.1    httr_1.4.1
[70] R6_2.4.1            multtest_2.44.0     compiler_4.0.0

Let me know if any other information are needed.

thanks

[Bionett]

Hello @sariya,

I could not reproduce this error:

BiocManager::install("MetaVolcanoR")
library(MetaVolcanoR)
data(diffexplist)
dge_list <- diffexplist[1:2]
print(lapply(dge_list, str))

'data.frame': 6573 obs. of 5 variables:
$ Symbol: chr "A1BG" "A1BG-AS1" "A1CF" "A2M" ...
$ Log2FC: num -0.7013 -0.2511 0.0333 0.835 0.0394 ...
$ pvalue: num 0.00014 0.00869 0.61599 0.01855 0.84322 ...
$ CI.L : num -1.009 -0.43 -0.104 0.157 -0.373 ...
$ CI.R : num -0.3938 -0.0716 0.1703 1.5133 0.4517 ...
'data.frame': 6573 obs. of 5 variables:
$ Symbol: chr "A1BG" "A1BG-AS1" "A1CF" "A2M" ...
$ Log2FC: num -0.00915 -0.00553 0.32861 0.5284 -0.41521 ...
$ pvalue: num 0.82633 0.8745 0.27179 0.00121 0.00283 ...
$ CI.L : num -0.0944 -0.0771 -0.2747 0.2317 -0.6726 ...
$ CI.R : num 0.0761 0.066 0.9319 0.8251 -0.1578 ...

meta_degs_comb <- combining_mv(diffexp=dge_list, pcriteria='pvalue', foldchangecol='Log2FC', genenamecol='Symbol', geneidcol=NULL, metafc='Mean', metathr=0.05, collaps=TRUE, jobname="MetaVolcano", outputfolder=".", draw='HTML')

class(meta_degs_comb)
[1] "MetaVolcano" attr(,"package") [1] "MetaVolcanoR"

meta_degs_comb@MetaVolcano

It plots a metavolcano.

It might be related to your dge_list object. Are there any missing values or duplicated genes?

I tried the lastest R version for this.

sessionInfo()
R version 4.0.2 (2020-06-22)

other attached packages:
[1] MetaVolcanoR_1.2.0

loaded via a namespace (and not attached):
[1] zoo_1.8-8 tidyselect_1.1.0 purrr_0.3.4
[4] TFisher_0.2.0 splines_4.0.2 lattice_0.20-41
[7] colorspace_1.4-1 vctrs_0.3.1 generics_0.0.2
[10] htmltools_0.5.0 stats4_4.0.2 viridisLite_0.3.0
[13] yaml_2.2.1 survival_3.1-12 plotly_4.9.2.1
[16] rlang_0.4.7 pillar_1.4.6 sn_1.6-2
[19] glue_1.4.1 withr_2.2.0 metap_1.3
[22] BiocGenerics_0.34.0 multcomp_1.4-13 lifecycle_0.2.0
[25] stringr_1.4.0 munsell_0.5.0 gtable_0.3.0
[28] htmlwidgets_1.5.1 mvtnorm_1.1-1 codetools_0.2-16
[31] Biobase_2.48.0 labeling_0.3 mutoss_0.1-12
[34] gbRd_0.4-11 crosstalk_1.1.0.1 metafor_2.4-0
[37] parallel_4.0.2 TH.data_1.0-10 Rcpp_1.0.5
[40] scales_1.1.1 BiocManager_1.30.10 plotrix_3.7-8
[43] jsonlite_1.7.0 tmvnsim_1.0-2 topconfects_1.4.0
[46] farver_2.0.3 mnormt_2.0.1 ggplot2_3.3.2
[49] digest_0.6.25 stringi_1.4.6 dplyr_1.0.0
[52] numDeriv_2016.8-1.1 cowplot_1.0.0 grid_4.0.2
[55] bibtex_0.4.2.2 Rdpack_1.0.0 tools_4.0.2
[58] sandwich_2.5-1 magrittr_1.5 lazyeval_0.2.2
[61] tibble_3.0.3 crayon_1.3.4 tidyr_1.1.0
[64] pkgconfig_2.0.3 MASS_7.3-51.6 ellipsis_0.3.1
[67] Matrix_1.2-18 data.table_1.12.8 assertthat_0.2.1
[70] httr_1.4.1 R6_2.4.1 multtest_2.44.0
[73] nlme_3.1-148 compiler_4.0.2

[complexgenome]

hi bionett,

Thanks for looking into this. It works totally fine with the sample dataset. When I run the following command, a .html file is produced (volcano plot)

 meta_degs_comb <- combining_mv(diffexp=dge_list, pcriteria='pvalue',
                    foldchangecol='Log2FC', genenamecol='Symbol',
                    geneidcol=NULL,metafc='Mean',metathr=0.05,collaps=TRUE,                   jobname="MetaVolcano",
                    outputfolder=".",    draw='HTML')

Error:

Error in validObject(.Object) :
  invalid class "MetaVolcano" object: invalid object for slot "inputnames" in class "MetaVolcano": got class "NULL", should be or extend class "character"
In addition: There were 50 or more warnings (use warnings() to see the first 50)

Also, when I try to dissect output object as below, I get error

class(meta_degs_comb)
Error: object 'meta_degs_comb' not found

Item 1 in list has 14,385 genes, where as item 2 in list has 15,344 genes; their intersection is of 13,940 genes. I thought maybe genes missing in one item or vice-versa are causing this. In order to test that, I next work with genes that are found in both items of the list. That also gets me to the error:

Error in validObject(.Object) :
  invalid class "MetaVolcano" object: invalid object for slot "inputnames" in class "MetaVolcano": got class "NULL", should be or extend class "character"

Edit: there are no duplicate genes. Also, there was row with "NA" I removed it from both items in the list, work with overlapping genes only, still the error persists.

[Bionett]

@sariya could you share your input list? so I could reproduce this error.

[AnaBVA]

I had the same problem!!

After checking NA values and duplicated genes, I realized the error is because the list needed names per element. At the end of the function rem_mv.R , the object MetaVolcano is created using: inputnames=names(diffexp). In this case, check names(dge_list) and it shouldn't be NULL.

[Close-your-eyes]

So, almost 2 years have passed. No update.
The fix to the error was easy to find, but also adding a check to the function whether the diffexp-list has names would be very simple.
Why dont you add a check at the beginning of the function?!