I'm having difficulties in creating a Summarised Experiment object with my data. I need this object to proceed with the scDD package. The instructions in the Vignettes of the scDD package are not very clear to me. Can anyone help?
Have you looked at the SummarizedExperiment vignette? There is a section titled 'Constructing a SummarizedExperiment' that might apply here.
I've used TCGAbiolinks to create a SummarizedExperiment from the data available at the GDC. It might also be useful for working with files you have already downloaded, but I have not tried that.
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version 2.3.6
It would help if you could give some information on why you are not able to construct the SummarizedExperiment object. What have you tried? Which part is giving you trouble? What format is your data currently in? Have you tried going through the examples in the SummarizedExperiment package?
I've finally been able to create a SummarizedExperiment object but the assay slot is not empty. Thus, I cannot use the object to create a SingleCellExperiment object as input for the scDD package. I've tried creating the SingleCellExperiment object directly from my dataframe. Again, I'm having issues with the assays slot and the colData slot.
With my data, I cannot use the functions in the section 'Constructing a SummarizedExperiment' of the SummarizedExperiment vignette. I think my data might not be in the same format as the SD but I cannot create the SD object since the Rstudio keeps crashing every time I try.
My data comprises of log2 values of gene expression. The rows correspond the genes and the columns the samples. My dataset file is in csv format. I've tried going through the examples but I'm still having issues with the assays slot and the colData slot.
I'd guess that the class of the argument that you are trying to set the assay to is a data.frame; try with a matrix.
It's very hard to tell what difficulties you are having without something in the way of code.
I've been able to fix the colData issue. Now the problem is the NormCounts slot of the Assays. The class of the assay argument is a matrix. Below is the script I'm using and the error message I'm getting. CSCall is my dataset (table with gene names as rownames and sample names as column names) and condition is my dataframe with one column with only my conditions (no rownames).
> log2values <- as.matrix(CSCall)
> sce <- SingleCellExperiment(assays= list(Normcounts=log2values, Counts=log2values), colData=(condition))
> prior_param=list(alpha=0.01, mu0=0, s0=0.01, a0=0.01, b0=0.01)
> SCE <- scDD(sce, prior_param = prior_param, testZeroes = F, permutations=100)
Error in scDD(sce, prior_param = prior_param, testZeroes = F, permutations = 100) :
Please make sure the 'SingleCellExperiment' object includes an assays slot named 'normcounts' that contains normalized counts on the original scale
Thank you for your help
Looks like the expectation is that the assays should be named 'normcounts' rather than 'Normcounts', i.e., capitalization.