search

cole-trapnell-lab / monocle-release

277 stars 116 forks source link

error......> cds <- estimateSizeFactors(cds) #276

Open kasumaz opened 5 years ago

kasumaz commented 5 years ago

Hi, Just gone through the tutorial with the Paul et al data At this step: http://cole-trapnell-lab.github.io/monocle-release/monocle3/#step-1-noramlize-and-pre-process-the-data

I am loading in my own data and attempting to run. I have the following error:

cds <- estimateSizeFactors(cds) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘estimateSizeFactors’ for signature ‘"data.frame"’

i read in a .csv file with the genes in row, 1 row as gene symbols and columns as single cells. All as a matrix of course.

Any help here would be really appreciated. Regards

ChengxiangQiu commented 5 years ago
  1. are you sure that you correctly install and load monocle package? 2. are you sure that your monocle object ("cds") is correct? You need to create a monocle object first, rather than a simple data matrix.
kasumaz commented 5 years ago

Hi, Thanks for your reply. Indeed the monocle package is loaded. I think i am having problems first with creating an object. I run this:

matrix <- read.table("MatrixNorm.csv") sample <- read.table("sample.csv") gene_ann <- read.table("gene_annotation.csv") pd <- new("AnnotatedDataFrame", data = sample) fd <- new("AnnotatedDataFrame", data = gene_ann) cds <- new("CellDataSet", exprs = as.matrix(matrix), phenoData = pd, featureData = fd)

The error is that: Error in validObject(.Object) : invalid class “CellDataSet” object: sampleNames differ between assayData and phenoData

I went back my files to check that the rows for the gene annotation and matrix are the same. I used a normalised matrix too this time. Also to check and see if the column size is the same and corresponds to the same size as the matrix. I uploaded a smaller matrix incase you would like to see. I see that there are other threads but without a solution. Any further help would be massively appreciated. Thank you. Tutorial.zip

davisidarta commented 4 years ago

I'm having exactly the same issue as @kasumaz, with the exception I'm sure the cds data I'm loading is absolutely fine - It's a subsampled 100k cells from the Mouse Organogenesis Cell Atlas (https://oncoscape.v3.sttrcancer.org/atlas.gs.washington.edu.mouse.rna/downloads).

I've also installed monocle3 as oriented.


>#Load Organogenesis dataset
>library(monocle3)

>cds <- readRDS('cds_cleaned_sampled_100k.RDS')
>exp <- exprs(cds)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘exprs’ for signature ‘"CellDataSet"’

Any insight from the developers in making their public data actually acessible?