Issue with FindDE

[UConnMiura]

I’ve been trying out the tutorials, and encountered an error when trying Differential Expression analysis. SCAPE::FindDE

This is the tutorial in questions:
https://github.com/LuChenLab/SCAPE/blob/main/tutorial/Tutorial.md

When I run this:

de_res <- SCAPE::FindDE(
gene_obj,
idents.1 = 'Erythroblast',
idents.2 = 'Myelinating_oligodendrocyte',
annot = annot_info,
assay = "apa",
cores = 20
)

The error message I get is:

converting counts to integer mode
Error in estimateExonFoldChanges(., BPPARAM = BPPARAM) :
could not find function "estimateExonFoldChanges"
In addition: Warning message:
In DESeqDataSet(rse, design, ignoreRank = TRUE) :
some variables in design formula are characters, converting to factors

I am running the software on a laptop (mac) using R studio.
I installed the R library SCAPE using devtools, install_local(“…/SCAPE.R”)

I see that estimateExonFoldChanges is a Dexseq. Perhaps the DifferentialTest.R file needs to be altered?

Thanks in advance for any help you can provide.

Best,

Pedro Miura

[zhou-ran]

Hi Pedro,

Sorry for this bug, we updated a new version for this error. And we recommend you perform the DE analysis on laptop with 1 core.

Best,
Ran

[UConnMiura]

Thanks so much. It works for me now. Pedro Miura Associate Professor Dept. of Genetics and Genome Sciences UConn Health https://www.post-transcriptional.com/ From: Ran Zhou ***@***.***> Date: Tuesday, April 11, 2023 at 1:14 AM To: LuChenLab/SCAPE ***@***.***> Cc: Miura,Pedro ***@***.***>, Author ***@***.***> Subject: Re: [LuChenLab/SCAPE] Issue with FindDE (Issue #9) *** Attention: This is an external email. Use caution responding, opening attachments or clicking on links. *** Hi Pedro, Sorry for this bug, we updated a new version for this error. And we recommend you perform the DE analysis on laptop with 1 core. Best, Ran — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/LuChenLab/SCAPE/issues/9*issuecomment-1502699843__;Iw!!Cn_UX_p3!jCvpds-UCb7xEF0pYrI330PRpdHB76p3scU_JgGN3GBCQp9rJC_vPvvFoDOvvf3rjNzismJ_i-57p9jNOf8cgA$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/A67WYUFDWZT57ZU4Y7VH3JLXATSENANCNFSM6AAAAAAWZM46NY__;!!Cn_UX_p3!jCvpds-UCb7xEF0pYrI330PRpdHB76p3scU_JgGN3GBCQp9rJC_vPvvFoDOvvf3rjNzismJ_i-57p9gYZW3v5g$>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[UConnMiura]

Hi Ran, One more question. For the installation of SCAPE on an HPC there is a requirement for R to be installed. But this is not reflected in the installation instructions. https://github.com/LuChenLab/SCAPE Is there an r-base version that you recommend to install via conda? I’ve tried several installations of R via conda and have had no success. These are the errors I get after trying to run: python SCAPE/main.py --help Traceback (most recent call last): File "SCAPE/main.py", line 1, in <module> from cli.cli import cli File "/labs/Miura/pedro/scape_2/SCAPE/cli/cli.py", line 4, in <module> from cli.apamix import apamix File "/labs/Miura/pedro/scape_2/SCAPE/cli/apamix.py", line 19, in <module> from apamix.inference import wraper_process File "/labs/Miura/pedro/scape_2/SCAPE/apamix/inference.py", line 11, in <module> from apamix.apamix import APA File "/labs/Miura/pedro/scape_2/SCAPE/apamix/apamix.py", line 11, in <module> from rpy2.robjects.packages import STAP File "/home/FCAM/pmiura/miniconda3/envs/scape/lib/python3.7/site-packages/rpy2/robjects/__init__.py", line 19, in <module> from rpy2.robjects.robject import RObjectMixin, RObject File "/home/FCAM/pmiura/miniconda3/envs/scape/lib/python3.7/site-packages/rpy2/robjects/robject.py", line 10, in <module> rpy2.rinterface.initr_simple() File "/home/FCAM/pmiura/miniconda3/envs/scape/lib/python3.7/site-packages/rpy2/rinterface.py", line 798, in initr_simple status = embedded._initr() File "/home/FCAM/pmiura/miniconda3/envs/scape/lib/python3.7/site-packages/rpy2/rinterface_lib/embedded.py", line 119, in _initr raise ValueError('openrlib.R_HOME cannot be None.') ValueError: openrlib.R_HOME cannot be None. Thanks, Pedro Pedro Miura Associate Professor Dept. of Genetics and Genome Sciences UConn Health https://www.post-transcriptional.com/ From: Miura,Pedro ***@***.***> Date: Tuesday, April 11, 2023 at 10:50 AM To: LuChenLab/SCAPE ***@***.***> Subject: Re: [LuChenLab/SCAPE] Issue with FindDE (Issue #9) Thanks so much. It works for me now. Pedro Miura Associate Professor Dept. of Genetics and Genome Sciences UConn Health https://www.post-transcriptional.com/ From: Ran Zhou ***@***.***> Date: Tuesday, April 11, 2023 at 1:14 AM To: LuChenLab/SCAPE ***@***.***> Cc: Miura,Pedro ***@***.***>, Author ***@***.***> Subject: Re: [LuChenLab/SCAPE] Issue with FindDE (Issue #9) *** Attention: This is an external email. Use caution responding, opening attachments or clicking on links. *** Hi Pedro, Sorry for this bug, we updated a new version for this error. And we recommend you perform the DE analysis on laptop with 1 core. Best, Ran — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/LuChenLab/SCAPE/issues/9*issuecomment-1502699843__;Iw!!Cn_UX_p3!jCvpds-UCb7xEF0pYrI330PRpdHB76p3scU_JgGN3GBCQp9rJC_vPvvFoDOvvf3rjNzismJ_i-57p9jNOf8cgA$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/A67WYUFDWZT57ZU4Y7VH3JLXATSENANCNFSM6AAAAAAWZM46NY__;!!Cn_UX_p3!jCvpds-UCb7xEF0pYrI330PRpdHB76p3scU_JgGN3GBCQp9rJC_vPvvFoDOvvf3rjNzismJ_i-57p9gYZW3v5g$>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[UConnMiura]

Hi Ran, I solved this. In case you want to correct it on the github. By modifying requirements.txt to include: r-base==4.1.2 on the first line, it now runs. Thanks, Pedro Miura Associate Professor Dept. of Genetics and Genome Sciences UConn Health https://www.post-transcriptional.com/ From: Miura,Pedro ***@***.***> Date: Thursday, April 13, 2023 at 1:20 PM To: LuChenLab/SCAPE ***@***.***> Subject: Re: [LuChenLab/SCAPE] Issue with FindDE (Issue #9) Hi Ran, One more question. For the installation of SCAPE on an HPC there is a requirement for R to be installed. But this is not reflected in the installation instructions. https://github.com/LuChenLab/SCAPE Is there an r-base version that you recommend to install via conda? I’ve tried several installations of R via conda and have had no success. These are the errors I get after trying to run: python SCAPE/main.py --help Traceback (most recent call last): File "SCAPE/main.py", line 1, in <module> from cli.cli import cli File "/labs/Miura/pedro/scape_2/SCAPE/cli/cli.py", line 4, in <module> from cli.apamix import apamix File "/labs/Miura/pedro/scape_2/SCAPE/cli/apamix.py", line 19, in <module> from apamix.inference import wraper_process File "/labs/Miura/pedro/scape_2/SCAPE/apamix/inference.py", line 11, in <module> from apamix.apamix import APA File "/labs/Miura/pedro/scape_2/SCAPE/apamix/apamix.py", line 11, in <module> from rpy2.robjects.packages import STAP File "/home/FCAM/pmiura/miniconda3/envs/scape/lib/python3.7/site-packages/rpy2/robjects/__init__.py", line 19, in <module> from rpy2.robjects.robject import RObjectMixin, RObject File "/home/FCAM/pmiura/miniconda3/envs/scape/lib/python3.7/site-packages/rpy2/robjects/robject.py", line 10, in <module> rpy2.rinterface.initr_simple() File "/home/FCAM/pmiura/miniconda3/envs/scape/lib/python3.7/site-packages/rpy2/rinterface.py", line 798, in initr_simple status = embedded._initr() File "/home/FCAM/pmiura/miniconda3/envs/scape/lib/python3.7/site-packages/rpy2/rinterface_lib/embedded.py", line 119, in _initr raise ValueError('openrlib.R_HOME cannot be None.') ValueError: openrlib.R_HOME cannot be None. Thanks, Pedro Pedro Miura Associate Professor Dept. of Genetics and Genome Sciences UConn Health https://www.post-transcriptional.com/ From: Miura,Pedro ***@***.***> Date: Tuesday, April 11, 2023 at 10:50 AM To: LuChenLab/SCAPE ***@***.***> Subject: Re: [LuChenLab/SCAPE] Issue with FindDE (Issue #9) Thanks so much. It works for me now. Pedro Miura Associate Professor Dept. of Genetics and Genome Sciences UConn Health https://www.post-transcriptional.com/ From: Ran Zhou ***@***.***> Date: Tuesday, April 11, 2023 at 1:14 AM To: LuChenLab/SCAPE ***@***.***> Cc: Miura,Pedro ***@***.***>, Author ***@***.***> Subject: Re: [LuChenLab/SCAPE] Issue with FindDE (Issue #9) *** Attention: This is an external email. Use caution responding, opening attachments or clicking on links. *** Hi Pedro, Sorry for this bug, we updated a new version for this error. And we recommend you perform the DE analysis on laptop with 1 core. Best, Ran — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/LuChenLab/SCAPE/issues/9*issuecomment-1502699843__;Iw!!Cn_UX_p3!jCvpds-UCb7xEF0pYrI330PRpdHB76p3scU_JgGN3GBCQp9rJC_vPvvFoDOvvf3rjNzismJ_i-57p9jNOf8cgA$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/A67WYUFDWZT57ZU4Y7VH3JLXATSENANCNFSM6AAAAAAWZM46NY__;!!Cn_UX_p3!jCvpds-UCb7xEF0pYrI330PRpdHB76p3scU_JgGN3GBCQp9rJC_vPvvFoDOvvf3rjNzismJ_i-57p9gYZW3v5g$>. You are receiving this because you authored the thread.Message ID: ***@***.***>