Comments (2)
Hi Jane,
could it be that there are two many NAs in the data to cluster? Try do the same plot without clustering and you should be able to see it.
Best,
Ricard.
P.S. We have recently released MOFA v2 (https://github.com/bioFAM/MOFA2). Although there are novel functionalities, you can still train MOFA v1 models (but faster and with better downstream analysis functions).
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Thank you for your answer.
I did the same plot without clustering (cluster_rows=FALSE, cluster_cols = FALSE) and got no error.
Also, I did the same using clustering on columns only and this is also fine.
But clustering on rows leads to the same error. Which does not held anymore if I use Euclidean distance.
I do not understand why the clustering on columns only is fine and not on rows.
Neither why does it change depending on the distance. Computing Euclidean or correlation distances across genes or across samples give differences...
Thank you for mentioning the v2, I might take a look at it in the near future
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Related Issues (20)
- errors in installing MOFA HOT 2
- Improving memory efficiency for CITE-seq data analysis HOT 5
- AttributeError: module 'mofapy' has no attribute 'core.entry_point' HOT 4
- Documentation missmatch for getDefaultModelOptions()$numFactors HOT 1
- MOFA2: IndexError: list index out of range HOT 1
- Question on initialization HOT 2
- Issue with runMOFA(object) HOT 1
- Error in py_call_impl(callable, dots$args, dots$keywords) : AttributeError: 'NoneType' object has no attribute 'getExpectations' HOT 1
- Failure to Capture Common Sources of Variance in Data HOT 1
- error message: mofapy package not found. HOT 2
- AssertionError: dimensionality mismatch HOT 1
- Different data processing on metabolomics, I get different R2. HOT 7
- Thanks. another problem on running MOFA
- Problem to use mofaOBJECT HOT 2
- Problem to use plotVarianceExplained object in ggplot2
- Error in py_call_impl(callable, dots$args, dots$keywords) : UnicodeEncodeError: 'ascii' codec can't encode character '\u03b5' in position 5: ordinal not in range(128)
- predict function should use S3 dispatching
- 'MOFAtools'
- Archive this repo
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