Showing : delayedarray • reset
3
votes
8
replies
3.0k
views
Tutorial: "developing" with HDF5Array
hdf5 DelayedArray summarizedexperiment Tutorial
7.2 years ago Vincent J. Carey, Jr. 6.7k
2
votes
8
replies
2.4k
views
DelayedArray loading Warning causes stop in Bioconductor 3.12
DelayedArray warning installation
updated 3.9 years ago by 16k • written 3.9 years ago by ▴ 10
4
votes
1
reply
2.1k
views
How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
20 months ago merv ▴ 120
0
votes
1
reply
1.8k
views
DESeq2 in R 4.2.2
DESeq2 SummarizedExperiment DelayedArray
updated 15 months ago by ★ 4.0k • written 15 months ago by • 0
1
vote
1
reply
1.8k
views
Problem installing DelayedArray
DelayedArray
updated 3.2 years ago by 16k • written 3.2 years ago by ★ 8.2k
4
votes
13
replies
1.8k
views
Speeding up of DelayedArray::write_block()
HDF5Array DelayedArray
updated 6 months ago by 16k • written 2.6 years ago by ▴ 10
0
votes
1
reply
1.8k
views
Installation of package DelayedArray had non-zero exit status
delayedarray
5.8 years ago cristoforo-grasso • 0
1
vote
6
replies
1.7k
views
Unusually long running times for getMeth function since latest release
bsseq delayedarray
updated 6.8 years ago by ▴ 740 • written 6.8 years ago by ★ 1.9k
8
votes
8
replies
1.7k
views
DelayedArray seeds: SolidRleArraySeed vs ChunkedRleArraySeed vs DataFrame of Rle's
delayedarray delayedmatrixstats
updated 5.5 years ago by ▴ 740 • written 5.5 years ago by ▴ 170
1
vote
3
replies
1.7k
views
Troubles with barcodeRanks()
DropletUtils SingleCellExperiement DelayedArray simpleSingleCell
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 170
1
vote
5
replies
1.6k
views
rowsum or similar for RleArray?
delayedarray rowsum
written 6.6 years ago by ▴ 170
2
votes
4
replies
1.6k
views
SummarizedExperiment is now warning on attach about `read_block` namespace conflict
SummarizedExperiment S4Arrays DelayedArray
updated 10 months ago by 16k • written 11 months ago by ▴ 90
7
votes
4
replies
1.6k
views
From RleList to RleArray
delayedarray rlelist rle
updated 6.5 years ago by ▴ 740 • written 6.5 years ago by ▴ 950
2
votes
3
replies
1.6k
views
Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
19 months ago merv ▴ 120
2
votes
6
replies
1.5k
views
"dim<-" against on-disk arrays
DelayedArray TileDBArray HDF5Array
updated 2.9 years ago by 16k • written 3.0 years ago by ▴ 10
2
votes
6
replies
1.5k
views
Plans for multicore block processing in DelayedArray?
delayedarray
updated 6.6 years ago by 16k • written 6.6 years ago by ▴ 170
9
votes
8
replies
1.4k
views
Processing time of blockApply and DelayedArray
DelayedArray HDF5Array
updated 2.9 years ago by 16k • written 2.9 years ago by ▴ 40
4
votes
4
replies
1.4k
views
remove NA's from a DelayedArray
delayedarray
updated 6.6 years ago by 16k • written 6.6 years ago by ▴ 170
3
votes
5
replies
1.3k
views
Block processing matrices of different dimensions with DelayedArray
HDF5Array DelayedArray
updated 2.9 years ago by 16k • written 2.9 years ago by ▴ 40
0
votes
1
reply
1.3k
views
Error with dmrfinder bsseq after combining Bsseq obj
bsseq r package dmrfinder delayedarray combine
6.8 years ago br • 0
2
votes
2
replies
1.2k
views
how to combine multiple DelayedArray to a high dimension array
delayedarray
updated 6.1 years ago by ▴ 740 • written 6.1 years ago by ★ 1.3k
2
votes
1
reply
1.2k
views
scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
scater BiocSingular DelayedArray
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 350
1
vote
2
replies
1.1k
views
Error: C stack usage of HDF5Array
DelayedArray HDF5Array
3.0 years ago Koki ▴ 10
2
votes
3
replies
1.1k
views
Generating a DelayedArray with a size greater than .Machine$integer.max
bit64 HDF5Array DelayedArray
updated 2.8 years ago by 16k • written 2.9 years ago by ▴ 10
2
votes
4
replies
1.1k
views
`aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size aware?
HDF5Array DelayedArray
2.9 years ago Koki ▴ 10
0
votes
1
reply
1.1k
views
DelayedArray install fails to UNC path
delayedarray bug installation
updated 5.7 years ago by 25k • written 5.8 years ago by • 0
4
votes
3
replies
1.1k
views
Best way of creating a large RleMatrix
DelayedArray RleMatrix
updated 5.3 years ago by 16k • written 5.4 years ago by ▴ 170
4
votes
3
replies
1.1k
views
Temporal directory setting for DelayedArray
HDF5Array DelayedArray
2.8 years ago Koki ▴ 10
0
votes
8
replies
1.0k
views
Support of parquet files for on-disk Bioconductor objects
DelayedArray TileDBArray
7 months ago sandmann.t ▴ 70
0
votes
0
replies
1.0k
views
Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
20 months ago merv ▴ 120
1
vote
1
reply
1.0k
views
Could not find function ".read_block_OLD"
DelayedArray S4Arrays
updated 11 months ago by 16k • written 11 months ago by • 0
6
votes
5
replies
974
views
Building an HDF5Array/DelayedArray object incrementally
delayedarray
updated 3.6 years ago by 65k • written 3.6 years ago by ▴ 590
2
votes
5
replies
900
views
SparseArray unable to install on Bioc 3.18
DESeq2 SummarizedExperiment SparseArray Install DelayedArray
updated 5 months ago by 41k • written 5 months ago by • 0
0
votes
1
reply
870
views
How to incrementaly load the nzdata and nzindex from SparseArraySeed
TileDBArray HDF5Array DelayedArray
2.9 years ago Koki ▴ 10
1
vote
6
replies
763
views
DelayedArray::read_sparse_block
DelayedArray
updated 7 months ago by 16k • written 8 months ago by ▴ 10
0
votes
1
reply
730
views
Error in 1D DelayedArray, when the spacings is larger than 1
DelayedArray
2.9 years ago Koki ▴ 10
36 results • Page 1 of 1
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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