Closed andhartm closed 5 years ago
Hi Andreas
Thanks for your question. This is a "warning" that does not affect clust's run or results. I will try to suppress it in future releases.
Clust interpolates those N/A values with spline interpolation. If you feel that some rows have too many N/A values, it might make sense to filter them out.
I hope this answers your questions.
Please let me know if you have other questions. Best wishes, Basel
Hi Basel,
Thanks for the quick response. This answers my questions! Will try to filter my data a bit more.
Cheers, Andreas
First of all thanks for this great tool! My data files have missing values for quite a number of genes (set to N/A). When running these data files I get an error message but clust is still finishing the run. Removing all rows containing N/A values works but I don't want to loose all the data.
Error message: c:[ ].py:19: RuntimeWarning: invalid value encountered in greater I = np.bitwise_and(~isnan(X), X>0) c:[ ].py:465: RuntimeWarning: invalid value encountered in power Xnew[l][ogi] = np.log2(np.sum(np.power(2.0, Xloc[l][np.in1d(OGsDatasets[l], og)]), axis=0))
Data: GeneID | Treatment 1 | Treatment 2 | Treatment 3 | Treatment 4 | Treatment 5 | Treatment 6 1 | 4.273093893 | 0 | 1.946402008 | 1.374515554 | 2.655817399 | 5.267132206 2 | 5.956198005 | N/A | N/A | N/A | N/A | 5.266617765 3 | N/A | 0 | N/A | 0 | N/A | 5.264203631 4 | 0 | 0 | N/A | 0 | N/A | 5.261192058 6 | 3.96170082 | 1.7741793 | 0 | 1.612520247 | 3.915867084 | 5.259103225 7 | 5.118588008 | 0 | 3.888582101 | 0 | 0 | 5.257160244 8 | 4.393112039 | 0 | N/A | N/A | N/A | 5.252373101 …
How to deal with this issue (N/A and leaving them blank gives the same error message)? How is clust dealing with this data? Does clust automatically remove these rows?
Thanks for your help!