Allow DEA to be performed on a subset of the samples#1627
Allow DEA to be performed on a subset of the samples#1627arteymix wants to merge 8 commits intohotfix-1.32.7from
Conversation
|
@maubermann this is relevant for you |
arteymix
force-pushed
the
feature-dea-on-sample-subset
branch
from
0c98f3f to
634727f
Compare
arteymix
force-pushed
the
feature-dea-on-sample-subset
branch
from
634727f to
8df721e
Compare
gemma-cli/src/main/java/ubic/gemma/apps/DifferentialExpressionAnalysisCli.java
Outdated
Show resolved
Hide resolved
gemma-cli/src/main/java/ubic/gemma/apps/DifferentialExpressionAnalysisCli.java
Outdated
Show resolved
Hide resolved
gemma-cli/src/main/java/ubic/gemma/cli/completion/CompletionType.java
Outdated
Show resolved
Hide resolved
gemma-core/src/main/java/ubic/gemma/core/analysis/expression/diff/LinearModelAnalyzer.java
Outdated
Show resolved
Hide resolved
|
@oganm you should trigger the integration tests with Jenkins is set up to report which stages of the build were performed, but it stopped working once I migrated to use @ppavlidis' token. |
|
samples currently only accepts IDs, full names (i.e. "GSE2018_bioMaterial_11|GSM36433" for sample 24 of GSE2018). Accessions don't seem to be working |
|
Using accessions and names have minor issues related to #1640 but using them as returned by Gemma samples endpoint or anything that relies on an ExpressionExperiment object should be fine |
|
@oganm we typically don't assign accessions to BioMaterial, but to BioAssay. I made this specifically for resolving samples, but you could add additional checks for assays too. |
gemma-cli/src/main/java/ubic/gemma/apps/DifferentialExpressionAnalysisCli.java
Show resolved
Hide resolved
gemma-cli/src/main/java/ubic/gemma/apps/DifferentialExpressionAnalysisCli.java
Show resolved
Hide resolved
gemma-cli/src/main/java/ubic/gemma/apps/DifferentialExpressionAnalysisCli.java
Outdated
Show resolved
Hide resolved
arteymix
force-pushed
the
feature-dea-on-sample-subset
branch
from
b1a8cd7 to
da82fa2
Compare
arteymix
force-pushed
the
feature-dea-on-sample-subset
branch
2 times, most recently
from
e5aeb0f to
d184f3d
Compare
arteymix
force-pushed
the
feature-dea-on-sample-subset
branch
from
d184f3d to
2019886
Compare
| } | ||
| return result; | ||
| } | ||
|
|
There was a problem hiding this comment.
@oganm I haven't tested these two queries, but the idea is to fetch all the samples with the assay they belong to.
3 participants
No description provided.