Showing : geoquery • reset
0
votes
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152
views
Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
8 weeks ago Arianna • 0
0
votes
2
replies
336
views
Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 5 months ago by 48k • written 5 months ago by • 0
0
votes
2
replies
291
views
Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 5 months ago by • 0 • written 6 months ago by • 0
0
votes
1
reply
303
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 7 months ago by 63k • written 7 months ago by • 0
0
votes
1
reply
288
views
empty values when extracting beta values using the GEOquery
GSE61380 GEOquery
updated 10 months ago by ▴ 720 • written 10 months ago by • 0
3
votes
2
replies
795
views
Unable to download supplementary files from GSE146963 using GEOquery
GEOquery
updated 13 months ago by 3.5k • written 13 months ago by ▴ 10
0
votes
1
reply
395
views
Regarding Installation of GEOquery
BiocManager installation GEOquery
updated 14 months ago by ▴ 720 • written 14 months ago by • 0
1
vote
5
replies
689
views
Can't read in CEL files
GEO GEOquery
15 months ago OE • 0
0
votes
2
replies
658
views
How to get colData with GEOquery to prepare for DEseq2
GEOquery DEseq2
16 months ago Yugang • 0
1
vote
1
reply
1.6k
views
Error in downloading GEO Supplementary files
GEOquery
updated 18 months ago by ▴ 90 • written 18 months ago by • 0
5
votes
7
replies
1.6k
views
GEO series matrix empty
GEOquery GEO
19 months ago gs.123 ▴ 20
3
votes
2
replies
837
views
GEOquery returning NAs as probe names
GEOquery
updated 20 months ago by 21k • written 20 months ago by ▴ 30
3
votes
23
replies
3.1k
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery VROOM
22 months ago array chip ▴ 420
1
vote
2
replies
1.8k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 22 months ago by 21k • written 22 months ago by ▴ 10
0
votes
1
reply
1.7k
views
Data frame with 0 columns and 0 rows
GEOquery
updated 22 months ago by ▴ 720 • written 22 months ago by • 0
2
votes
3
replies
880
views
Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 22 months ago by 13k • written 22 months ago by ▴ 50
6
votes
7
replies
1.7k
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 22 months ago by 63k • written 22 months ago by ▴ 50
1
vote
1
reply
857
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 2.0 years ago by 63k • written 2.0 years ago by ▴ 50
1
vote
1
reply
943
views
unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 2.2 years ago by 21k • written 2.2 years ago by ▴ 10
0
votes
1
reply
658
views
GEOquery
GEOquery
updated 2.3 years ago by ▴ 720 • written 2.3 years ago by ▴ 10
6
votes
5
replies
936
views
a problem of package ""
GEO GEOquery
updated 2.3 years ago by 16k • written 2.3 years ago by ▴ 20
2
votes
3
replies
708
views
Problem about Geoquery
GEO GEOquery
2.3 years ago sheldon19931016 ▴ 20
7
votes
5
replies
5.4k
views
Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 8.3 years ago by 21k
0
votes
5
replies
3.0k
views
assayData: 0 features
geoquery
updated 2.6 years ago by ▴ 10 • written 8.0 years ago by ▴ 230
3
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4
replies
978
views
when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery projectR
updated 2.7 years ago by 21k • written 2.7 years ago by ▴ 20
3
votes
1
reply
699
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray GSE22247 limma GEOquery IlluminaChip
updated 2.8 years ago by 48k • written 2.8 years ago by • 0
0
votes
2
replies
1.3k
views
Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error GEOquery
updated 2.9 years ago by 1.6k • written 2.9 years ago by • 0
6
votes
3
replies
1.0k
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 3.3 years ago by 21k • written 3.3 years ago by ▴ 40
1
vote
1
reply
845
views
Table expression data from GEO file
GEO expression GEOquery
updated 3.4 years ago by ★ 3.0k • written 3.4 years ago by • 0
5
votes
5
replies
903
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 3.5 years ago by 63k • written 3.5 years ago by ▴ 810
0
votes
1
reply
780
views
I have installed bioconductor, R still asks me to install it
bioconductor biocLite GEOquery package
updated 3.7 years ago by 13k • written 3.7 years ago by • 0
0
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3
replies
794
views
GEOquery and Feature data
GEOquery featureNames
updated 3.9 years ago by 21k • written 3.9 years ago by • 0
0
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3
replies
1.4k
views
When applying rma to featureset get error: 'package' must be of length 1
oligo biobase GEOquery
updated 3.9 years ago by 63k • written 3.9 years ago by ▴ 20
2
votes
2
replies
1.8k
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 3.9 years ago by 63k • written 3.9 years ago by ▴ 20
2
votes
1
reply
984
views
Downloading a private GEO with GEOquery
GEOquery
updated 4.0 years ago by 21k • written 4.0 years ago by ▴ 720
0
votes
5
replies
1.7k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 4.2 years ago by 63k • written 4.2 years ago by • 0
0
votes
0
replies
763
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 4.4 years ago by 63k • written 4.4 years ago by ▴ 10
3
votes
6
replies
2.5k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
4.4 years ago andy_shaps ▴ 10
1
vote
2
replies
978
views
How do I creat an expressionset if there is no GDS listed on the GEO database?
limma microarray GEOquery
updated 4.4 years ago by 63k • written 4.4 years ago by • 0
3
votes
4
replies
1.2k
views
GEOquery:Get error sampleNames
geoquery
updated 4.7 years ago by 0 • written 4.8 years ago by ▴ 10
2
votes
2
replies
1.8k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 4.8 years ago by 63k • written 4.8 years ago by ▴ 10
0
votes
2
replies
976
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
4.8 years ago cschot3 • 0
0
votes
0
replies
751
views
Query based on PMIDs
SRAdb geoquery
4.8 years ago Deepak Tanwar ▴ 10
5
votes
12
replies
2.2k
views
Using eset while parsing GSE file located in a path
GEO geoquery
updated 5.1 years ago by 21k • written 5.1 years ago by ▴ 20
2
votes
3
replies
1.4k
views
Filtering the probe set ids from GSE file
geoquery GSE
5.1 years ago mahm ▴ 20
3
votes
11
replies
1.9k
views
Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression geoquery GSE bioconductor microarray
updated 5.1 years ago by 21k • written 5.1 years ago by ▴ 20
3
votes
2
replies
1.5k
views
Installing GEOQuery failed with conda
geoquery anaconda libxml2
updated 5.1 years ago by 25k • written 5.1 years ago by ▴ 10
0
votes
1
reply
1.1k
views
question about getGEO function
geoquery
5.1 years ago maryam.sabet • 0
0
votes
1
reply
712
views
GEOquery install problem
geoquery
5.2 years ago 261092095 ▴ 10
3
votes
5
replies
2.1k
views
getGEO function doesn't download the expression data
geoquery
updated 5.2 years ago by ▴ 990 • written 5.2 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: DMRcate design by Jitendra ▴ 10
Thanks James, do I also need to mention 'contrasts=FALSE' in cpg.annotate.And also what to mentions in analysis.type="differential",/ "ANO…
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
I don't know the details but do you mean using `HDF5RealizationSink` or `TENxRealizationSink` will make it possible to writing sparse multi…
Comment: DelayedArray::read_sparse_block by Koki ▴ 10
Ok, I understood. How about "writing" to HDF5? Are you going to implement `write_block_as_sparse` in `SparseArray` package?
Comment: DelayedArray::read_sparse_block by Hervé Pagès 16k
> So do you means the specification change from DelayedArray's read_sparse_block to SparseArray's read_block_as_sparse will accelerate the …
Comment: DelayedArray::read_sparse_block by Koki ▴ 10
Thanks for your reply. So do you means the specification change from `DelayedArray`'s `read_sparse_block` to `SparseArray`'s `read_block_a…
Votes
Answer: DMRcate design
Answer: DMRcate design
Comment: DMRcate design
Answer: What MetaPhlAn3 database was used in cMD 3?
Comment: Speeding up of DelayedArray::write_block()
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