Open Tayyaba82 opened 3 years ago
Hi Tayyaba82, I could reproduce error 2 when each list in the 'lst' list object were NOT named. You must name them, e.g: lst=lst(data1=data1, data2=data2) I am not sure about error1, please check the format of your gene tables for formatting errors, these may be difficult to spot.
Hi Tayyaba82, I could reproduce error 2 when each list in the 'lst' list object were NOT named. You must name them, e.g: lst=lst(data1=data1, data2=data2) I am not sure about error1, please check the format of your gene tables for formatting errors, these may be difficult to spot.
Hello Judemt, can you please elaborate on how you solved this error?
Hi vinesh9727,
Error2: I table the entire output from fit2 in limma using the 'topTable' function, with confint=T and add a column of gene symbols that must have the same column name for each data set.
The input for 'rem_mv' requires a list of the topTable data frames for each data set in the meta-analysis, and these list objects must be named, hence; ListDatasets=list(data1=topTable1, data2=topTable2, etc...add the additional data set data frames)
Error1:
I have not used the 'votecount_mv' function, it seems the Regulation object was not added to the parameters and continuous limits were supplied to input data with a discrete scale but please check the vignette for this.
Sometimes errors can arise if there is a formatting problem with the input data, for example a gene symbol may have a hyphen (-) instead of an underscore (_). This is just meant as an example, I can't remember the specifics but I have had errors due to a formatting problem in a data frame and once corrected that solved the problem. So the root cause can be cryptic occasionally.
I hope this helps, please message if you need further clarification.
Hi vinesh9727,
Error2: I table the entire output from fit2 in limma using the 'topTable' function, with confint=T and add a column of gene symbols that must have the same column name for each data set.
The input for 'rem_mv' requires a list of the topTable data frames for each data set in the meta-analysis, and these list objects must be named, hence; ListDatasets=list(data1=topTable1, data2=topTable2, etc...add the additional data set data frames)
Error1:
I have not used the 'votecount_mv' function, it seems the Regulation object was not added to the parameters and continuous limits were supplied to input data with a discrete scale but please check the vignette for this.
Sometimes errors can arise if there is a formatting problem with the input data, for example a gene symbol may have a hyphen (-) instead of an underscore (_). This is just meant as an example, I can't remember the specifics but I have had errors due to a formatting problem in a data frame and once corrected that solved the problem. So the root cause can be cryptic occasionally.
I hope this helps, please message if you need further clarification.
Hello Judemt, Thank you so much for the response. I did the same error and now after naming each object I was able to get the results. I have one more question if you can help me with it, I would be extremely grateful. I tried to plot a forest plot after this where it considers the FC of a particular gene across studies. I am attaching the script of the tutorial which I have tried. So I wanted to ask can I add the summary p-value of that particular gene in the forest plot as I am unable to do so. Link for the tutorial :- https://rdrr.io/bioc/MetaVolcanoR/f/vignettes/MetaVolcano.Rmd The command for the forest plot function :- draw_forest(remres=meta_degs_rem, gene="MMP9", genecol="Symbol", foldchangecol="Log2FC", llcol="CI.L", rlcol="CI.R", jobname="MetaVolcano", outputfolder=".", draw="HTML")
Hello, I have the following errors while using MetaVolcanoR Pacakge. Error 1:
Error 2:
The data list used: head(lst) [[1]] Symbol log2FC pvalue CI.L CI.R 1 PRG2 9.821447 3.661549e-31 9.665207 9.977687 2 PTPRV 9.712034 4.291667e-31 9.556318 9.867750 3 A1BG 10.388674 1.064347e-30 10.214467 10.562881 4 A2M 9.760377 1.341346e-30 9.594825 9.925928 5 NAT1 8.521256 2.061779e-30 8.373620 8.668892 6 NAT2 8.711021 3.669413e-30 8.555737 8.866305 [[2]] Symbol log2FC pvalue CI.L CI.R 1 PRG2 9.463524 1.941380e-47 9.323093 9.603955 2 PTPRV 9.032391 2.149754e-47 8.897946 9.166836 3 A1BG 9.951994 2.345057e-47 9.803474 10.100515 4 A2M 10.724779 8.015122e-47 10.558701 10.890857 5 NAT1 9.541660 1.505059e-46 9.391078 9.692243 6 NAT2 10.023478 4.089614e-46 9.860465 10.186491