Comments (5)
Hi,
I I have figured out that it has actually nothing to do with SummarizedExperiment, but that it is indeed an issue with the latest version of RStudio. These messages show when you try to use $ on data.frames with more than 2000 columns. Sorry for the inconvenience!
from summarizedexperiment.
Hi @DijkJel
I am unable to reproduce this error on RELEASE_3_17
Bioconductor Docker container or in the terminal. Please make sure that BiocManager::valid()
is returning TRUE
.
Best,
Marcel
from summarizedexperiment.
Hi Marcel,
Thanks for the quick response. I have checked BiocManager::valid()
and it returns TRUE
. I think I've found the issue: the messages only appear when the colData exceeds 2000 columns.
For example, the following code works fine:
m = matrix(runif(100), 10, dimnames = list(NULL, letters[1:10]))
cd = as.data.frame(matrix(runif(2000*10), nrow = 10))
rownames(cd) = letters[1:10]
se = SummarizedExperiment(assays = list(a = m),
colData = cd)
se$
But when I increase the number of columns to 2001, it returns a warning and error:
m = matrix(runif(100), 10, dimnames = list(NULL, letters[1:10]))
cd = as.data.frame(matrix(runif(2001*10), nrow = 10))
rownames(cd) = letters[1:10]
se = SummarizedExperiment(assays = list(a = m),
colData = cd)
se$
Error in order(typeScores, scores) : argument lengths differ
In addition: Warning message:
In completions$type == .rs.acCompletionTypes$DATAFRAME & !completions$context %in% :
longer object length is not a multiple of shorter object length
Best,
Jelmer
from summarizedexperiment.
I can't reproduce this running R 4.3.1 with RStudio (Version 2023.06.0+421 (2023.06.0+421)) on macOS.
How are you running R? RStudio, R app, R from the command line, something else?
If something like RStudio, what version of that software are your running?
It may also help if you provide your sessionInfo()
after running your example and more details about your computer.
Here's mine
> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Australia/Melbourne
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] SummarizedExperiment_1.31.1 Biobase_2.61.0 GenomicRanges_1.53.1
[4] GenomeInfoDb_1.37.2 IRanges_2.35.2 S4Vectors_0.39.1
[7] BiocGenerics_0.47.0 MatrixGenerics_1.13.1 matrixStats_1.0.0
loaded via a namespace (and not attached):
[1] SparseArray_1.1.10 zlibbioc_1.47.0 Matrix_1.5-4.1
[4] lattice_0.21-8 GenomeInfoDbData_1.2.10 S4Arrays_1.1.4
[7] XVector_0.41.1 RCurl_1.98-1.12 bitops_1.0-7
[10] grid_4.3.1 DelayedArray_0.27.5 compiler_4.3.1
[13] rstudioapi_0.14 tools_4.3.1 BiocManager_1.30.21
[16] crayon_1.5.2
from summarizedexperiment.
Glad that you were able to narrow down the problem to a RStudio/data.frame issue. I guess we can close this then.
from summarizedexperiment.
Related Issues (20)
- Should the show() method for SummarizedExperiment objects suggest saveHDF5SummarizedExperiment()? HOT 1
- Enforce unique assay names HOT 2
- `combineCols()` and `combineRows()` not listed in 'Usage' section HOT 4
- Consider assayData DataFrame for assays HOT 6
- Constructor could check that assay is in matric format HOT 2
- `all.equal(x, y)` vs `all(x == y)` HOT 3
- Remove all dimnames in `combine_assays_by` to avoid constructor check failures HOT 3
- `combineCols` should keep names in metadata with `use.names=TRUE`
- Erroneous behaviour when colData is data.frame
- package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'SummarizedExperiment' HOT 1
- Add an `assaybind()` method
- Curious about how Rd manuals are generated HOT 3
- Feature request: keep rownames(se) and rownames() of DataFrame nested in rowData(se) in sync HOT 4
- metadata function is not exported as others HOT 1
- colData Default in Constructor Inconsistency HOT 1
- Warning about dim, nrow and ncol deprecated methods.
- Depreciated function calls in DelayedArray HOT 4
- Rows being removed from ASV table when building SummarizedExperiment
- Clarify withDimnames=FALSE in the documentation HOT 3
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from summarizedexperiment.