Closed beamilon closed 2 years ago
this needs to be re-uploaded, there is no umap coordinate in the observation file, the primary function will not work.
reupload the dataset again with tsne coordinate.
https://umgear.org/dataset_curator.html#/dataset/53f99080-29cd-44ca-4c14-b26ca1ad7588/displays
The primary is still not working. Since 221 was closed, I thought the dataset had been re-uploaded. Is there a different problem?
Is this still an issue? I can't see this dataset when I check the single-cell tool, though there is another whose name is very close (doesn't have the ", TSNE" part within the name).
The dataset in the public profile is the one without "TSNE": P25-P27, mouse, scRNA-seq, cochlear sensory neurons (Goodrich) There is a primary analysis available apparently but the 'Find marker genes' returns an error message.
@beamilon , the TSNE coordinate only adds to the one with TSNE in the title, the other one is for violin plot /svg purposes.
If you want to use the one with tsne, we should replace the one in the profile with the new one. without TSNE: c32835d3-cac4-bb0e-a90a-0b41dec6617a new with TSNE:53f99080-29cd-44ca-4c14-b26ca1ad7588
@songeric1107 Yes, I think we should replace with the new one to have access to the primary analysis
@beamilon @jorvis , this dataset is included in multiple profile, what is the best way to replace it.
scRNA-seq / Cell Types/Tissues / Andy / Neuron / SGNs / Neuron Total / Neuron / PMB SGNs / scRNAseq+deafenedRats / Tom / My Profile FW / test / single cell sq (interest) / Sian test / MyProfile01 / Neuron / Mouse cochlea Single-c RNAseq / SGN RNAseq c32835d3-cac4-bb0e-a90a-0b41dec6617a P25-P27, mouse, scRNA-seq, cochlear sensory neurons (Goodrich) single-cell-rnaseq rhertzano@smail.umaryland.ed30078709 GSE114997 Public 2019-01-31 18:37:40
So is that the only thing which has changed? tSNE was added but everything else stayed the same?
the column names are different, but the plot is the same
this dataset is included in multiple profiles, I am not sure whether other users have any curations using the old version.
@beamilon any comments?
@songeric1107 That's a good point. I will ask Ronna.
I'll bring convo back here. I checked and 5 different users have created curations for this dataset. If I can have a full list of the column names which have changed I can see which will break and correct them.
3 optional columns names for plotting: position(Apex,Base,Middle), tissue_type(1_A,1_B,1_C,T2), cluster_labe( Apex_1_A, Apex_1_B........Middle_1_A,Middle_1_B,Middle_1_C)
OK, so going from old to new, the changes are:
And I'm assuming cluster_label hasn't changed (or was it actually misspelled the first time as 'cluster_labe' ?
the cluster_label is different, the old one is the combination of the position+tissue_type; the cluster_label of the recent one is the same as the cell_type.
So the values within that column are different but the column name is the same. I think think there's anything to do with that one then.
I've replaced the h5 files with the new version and updated all the layout configs to reflect the new column names. Verified that displays still work:
And that marker genes now work:
The 53f99080-29cd-44ca-4c14-b26ca1ad7588 dataset can be deleted.
Sorry if I missed something and it is being taking care of, but the 'find marker genes' from the primary analysis for P25-P27, mouse, scRNA-seq, cochlear sensory neurons (Goodrich) returns an "Error reporting marker genes"