I am running the below code
pbmc.sce <- as.SingleCellExperiment(pbmc,assay = "RNA")
then i got this
Error in validityMethod(as(object, superClass)) :
object 'CsparseMatrix_validate' not found
in some old post, it ask us to update.packages("Matirx")
tried and didn't work for me. Your help would be much appreciated
Related
I just try to use :
scRNA <- FindNeighbors(scRNA, dims = pc.num)
and
scRNA.counts <- Read10X(data.dir = "filtered_feature_bc_matrix")
and both of them gives error like :
Error in validityMethod(as(object, superClass)) : object 'Matrix_validate' not found
I guess these code totally run well in other's computer
so I wonder what's wrong with my code and how to fix it ?
Indeed, to solve the problem for you, it should be sufficient to do what #Mikael Jagan says:
update.packages("Matrix")
2nd thought: The above may not solve the problem entirely:
As there are other packages involved, some of these may have to be re-installed (after the updating of Matrix).
Can you post the output (or good summary of that if it's too long) of
traceback()
immediately after producing the error you are seeing?
I am reading 2 vcf files in to R. They load fine (I have used 3 different methods to do this (read.vcf, readVCF, and fread) and all are fine) however when I go on to try and do anything with 1 of the vcf files, the msg reads:
Error in unlist_as_integer(x#subscript) : object 'fancy_mseq' not found
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'from': object 'fancy_mseq' not found
Usually I just google error msgs but I can not find anything online about this. Does anyone have any idea what could be causing this error message? Whilst it's hard to be 100% sure because of the vcf format, I can't see anything wrong with the file when I call str(), head() or any other ways of looking at the data.
Thank you!
When trying to run this (or any other) command
xtabs(ugdata$response, ugdata$Equity, data=ugdata)
I keep receiving this error
Error in formula.default(object, env = baseenv()) : invalid formula
I have been looking around all day, including similar posts on this website, but I cannot find a solution to help me fix this.
Any help would be greatly appreciated
I believe the error is in the syntax. Please try:
xtabs(ugdata$response ~ ugdata$Equity, data = ugdata)
I keep getting the error message
could not find function "Qrefine".
Got the error message when I keyed in the following in RStudio. Could someone help, please?
Qrefine.out <- Qrefine(data, Q_mis, gate="AND", max.ite=50)
print(Qrefine.out)
plot(Qrefine.out)
I am using mallet in R, It was working fine until I install devtools. After that I start getting following error which I never got.
Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, :
java.lang.NoSuchMethodException: No suitable method for the given parameters
error get thrown:
documents <- mallet.read.dir("~/mytopicsfiles/")
mallet.instances <- mallet.import(documents$id, documents$text, "~/stopwords.txt", token.regexp ="\\p{L}[\\p{L}\\p{P}]+\\p{L}")
After searching in, I found someone has answered exact question and answer given in that question did't actually work. Since its not an accepted answer not sure if the answer is correct.
rjava .jcall issue
Did you find the answer?
You should make documents$id and documents$text as character.
as.character(documents$id), as.character(documents$text)