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abort object when download from orchestra web instead of downloadPSet #138

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mugpeng opened this issue Feb 21, 2023 · 0 comments
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@mugpeng
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mugpeng commented Feb 21, 2023

Hi,

It's a very nice job you've done. But I found a bug here.

I downloaded the datasets from orchestra web, and I read it by readRDS then it outputs:

<PharmacoSet>
Name:  CTRPv2 
Date Created:  Tue Jun 23 23:32:05 2020 
Error in .local(object, ...) : 
  no slot of name "sample" for this object of class "PharmacoSet"
Error during wrapup: no slot of name "treatmentResponse" for this object of class "PharmacoSet"
Error: no more error handlers available (recursive errors?); invoking 'abort' restart

CTRP2 for example: https://orcestra.ca/pset/10.5281/zenodo.3905470

But I can successfully read the datasets when I download it by downloadPSet, here is Tavor dataset:

> tavor
<PharmacoSet>
Name:  Tavor 
Date Created:  Fri Feb  4 17:32:17 2022 
Number of samples:  53 
Molecular profiles:
RNAseq :
  Dim: 24137, 43 
Treatment response:
Drug pertubation:
   Please look at pertNumber(cSet) to determine number of experiments  for each drug-sample combination.
Drug sensitivity:
   Number of Experiments:  2668 
   Please look at sensNumber(cSet) to determine number of  experiments for each drug-sample combination.

And If I save it as a Rds, It could also be read reproducibly.

Is there anything wrong with the file on orchestra?

@jjjermiah jjjermiah self-assigned this Apr 8, 2024
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