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pachterlab / sleuth

Differential analysis of RNA-Seq
http://pachterlab.github.io/sleuth
GNU General Public License v3.0
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sleuth_live error : "test" is not a valid character #216

Open fifdick opened 5 years ago

fifdick commented 5 years ago

Hi,

using sleuth 0.30.0 I experience trouble when using sleuth_live. Some plots throw error messages and weird behaviour. For example when trying to look at the scatter plot I get the following error:

cannot coerce class 'c("quosure", "formula")' to a data.frame For most other plots like the qq plot:

'test' is not a valid character.

All plots and tables from the summaries tab work fine as well as PCA and heatmap. Under analysis, the gene_view does throw the same error as the qq plot. The MA plot throws this error:

is not a valid label for a test. Please see valid models and tests using the functions 'models' and 'tests'. Remember to also correctly specify the test type.

This is the code I used to create the sleuth object:

so <- sleuth_prep(sfdata, target_mapping = tx2gene,num_cores = 14,extra_bootstrap_summary=TRUE)
so <- sleuth_fit(so,design_reduced,'reduced')
so <- sleuth_fit(so, design_full, 'full')
so <- sleuth_lrt(so, 'reduced', 'full')
so <- sleuth_wt(so,'condition1')

This is what my data looks like:

> head(tx2gene)                                                                                                                                                                                                                                                                                                                                                                       
                      target_id            HGNC                                                                                                                                                                                                                                                                                                                                       
ENST00000373020 ENST00000373020 ENSG00000000003                                                                                                                                                                                                                                                                                                                                       
ENST00000496771 ENST00000496771 ENSG00000000003                                                                                                                                                                                                                                                                                                                                       
ENST00000494424 ENST00000494424 ENSG00000000003                                                                                                                                                                                                                                                                                                                                       
ENST00000373031 ENST00000373031 ENSG00000000005                                                                                                                                                                                                                                                                                                                                       
ENST00000485971 ENST00000485971 ENSG00000000005
ENST00000371588 ENST00000371588 ENSG00000000419
> head(sfdata)
    sample condition rin age_years sex cells cohort     path
1 SL283611         1 6.4        86   M       0.07119706    N /dir/SL283611
2 SL283562        0 6.6        85   F       0.20742223    N /dir/SL283562
3 SL283563       1 8.7        84   M       0.04721335    N /dir/SL283563
4 SL283564         0 6.4        84   F       0.03532790    N /dir/SL283564
5 SL283565         1 7.2        84   F       0.06035152    N /dir/SL283565
6 SL283566         0 7.4        76   F       0.04048141    P /dir/SL283566
> design_reduced
~age_years + sex + cells + rin + cohort
> design_full
~condition + age_years + sex + cells + rin + cohort

sessionInfo.txt

feldman4 commented 5 years ago

Following the walkthrough, adding Wald tests, and trying the entries in the sleuth_live > analyses menu reproduces this error, and a sleuth of others:

Warning: Error in get_test: '' is not a valid label for a test. Please see valid models and tests using the functions 'models' and 'tests'. Remember to also correctly specify the test type.

Warning: Error in FUN: object 'mean_obs' not found

Warning: Error in : object 'sigma_sq' not found

Warning: Error in sleuth_results: 'test' is not a valid character.

Warning: Error in sleuth_results: 'wb' is not a valid character.

Warning: Error in FUN: object 'b' not found