Closed andreanuzzo closed 5 years ago
Hi Andrea,
Honestly, I barely use MultiAssayExperiment and I am not sure where the error comes from. Are you allowed to share the data? If so, can you join the Sack group and send me the object so I can have a look?
Alternatively, you can try build de MOFAobject using a list of matrices, each entry being an assay with features as rows and samples as columns. More details in the documentation of createMOFAobject
P.S. I notice that your three assays are quite "imbalanced" (i.e. transcriptomics has way too many features compared to the other assays). Sometimes this can be a problem as the small views get underrepresented in the factors, see the FAQ in the README file. I recommend you filter the RNA data to select informative features. For example, subset protein-coding genes, filter out non-expressed genes and then select the top ~2,000 most variable genes.
Thank you Ricard. I have sent you a DM on the Slack group. I know the data are imbalanced, I will massage the transcriptomics with DeSeq2, but I was just playing a bit with the package after reading the paper.
Thank you!
Solved it: my sampleMap had further samples and in a different order of samples compared to colData. Not a problem for the MultiAssayExperiment but a problem for the creation of the MOFA object, due to the hidden function that it calls.
Thanks for your help. Might be good to add a more informative error message.
Hi, Thank you for the great work! I am attempting to test MOFA on my datasets, but I have troubles in converting the MultiAssayExperiment object into the MOFA object.
The MAE object was built using the MAE constructor function, and contains 3 experiments, colData and sampleMaps
This is how it looks like
But then
I tried peeking into the createMOFAobject function but I can't seem to find the necessary line. If I run
assays(multiHMP2)
I getAnd the MOFA object works if I try to construct it with
list(assays(multiHMP2)[['metagenomics']], ...etc))
I am sure I am missing something in the construction of the object, but I'm not sure what. Thanks!