Showing : geoquery • reset
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Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 10 days ago by 58k • written 10 days ago by ▴ 40
1
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1
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98
views
unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 10 weeks ago by 21k • written 10 weeks ago by ▴ 10
0
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1
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152
views
GEOquery
GEOquery
updated 3 months ago by ▴ 150 • written 3 months ago by • 0
6
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5
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234
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a problem of package ""
GEO GEOquery
updated 4 months ago by 15k • written 4 months ago by ▴ 20
2
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3
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150
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Problem about Geoquery
GEO GEOquery
4 months ago sheldon19931016 ▴ 20
7
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3
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3.3k
views
Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
6.3 years ago • updated 10 weeks ago Sean Davis 21k
0
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5
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1.4k
views
assayData: 0 features
geoquery
updated 6 months ago by • 0 • written 6.0 years ago by ▴ 230
3
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4
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350
views
when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery projectR
updated 7 months ago by 21k • written 8 months ago by ▴ 20
3
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1
reply
208
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray GSE22247 limma GEOquery IlluminaChip
updated 9 months ago by 43k • written 9 months ago by • 0
0
votes
2
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377
views
Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error GEOquery
updated 11 months ago by 1.5k • written 11 months ago by • 0
6
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3
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335
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 15 months ago by 21k • written 15 months ago by ▴ 40
1
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1
reply
186
views
Table expression data from GEO file
GEO expression GEOquery
updated 17 months ago by ★ 2.7k • written 17 months ago by • 0
4
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5
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305
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Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 18 months ago by 58k • written 18 months ago by ▴ 780
0
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1
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255
views
I have installed bioconductor, R still asks me to install it
bioconductor biocLite GEOquery package
updated 20 months ago by 13k • written 20 months ago by • 0
0
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3
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243
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GEOquery and Feature data
GEOquery featureNames
updated 22 months ago by 21k • written 22 months ago by • 0
0
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3
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536
views
When applying rma to featureset get error: 'package' must be of length 1
oligo biobase GEOquery
updated 23 months ago by 58k • written 23 months ago by ▴ 20
2
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2
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633
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 23 months ago by 58k • written 23 months ago by ▴ 20
2
votes
1
reply
291
views
Downloading a private GEO with GEOquery
GEOquery
updated 23 months ago by 21k • written 23 months ago by ▴ 650
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5
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848
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 2.2 years ago by 58k • written 2.2 years ago by • 0
0
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0
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321
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GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 2.4 years ago by 58k • written 2.4 years ago by ▴ 10
3
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6
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1.1k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
2.4 years ago andy_shaps ▴ 10
1
vote
2
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431
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How do I creat an expressionset if there is no GDS listed on the GEO database?
limma microarray GEOquery
updated 2.4 years ago by 58k • written 2.4 years ago by • 0
3
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4
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710
views
GEOquery:Get error sampleNames
geoquery
updated 2.7 years ago by 0 • written 2.8 years ago by ▴ 10
2
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2
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1.3k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 2.8 years ago by 58k • written 2.8 years ago by ▴ 10
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2
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484
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
2.8 years ago cschot3 • 0
0
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0
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389
views
Query based on PMIDs
SRAdb geoquery
2.8 years ago Deepak Tanwar ▴ 10
5
votes
12
replies
906
views
Using eset while parsing GSE file located in a path
GEO geoquery
updated 3.1 years ago by 21k • written 3.1 years ago by ▴ 20
2
votes
3
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599
views
Filtering the probe set ids from GSE file
geoquery GSE
3.1 years ago mahm ▴ 20
3
votes
11
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943
views
Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression geoquery GSE bioconductor microarray
updated 3.1 years ago by 21k • written 3.1 years ago by ▴ 20
3
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2
replies
654
views
Installing GEOQuery failed with conda
geoquery anaconda libxml2
updated 3.1 years ago by 25k • written 3.1 years ago by ▴ 10
0
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1
reply
630
views
question about getGEO function
geoquery
3.1 years ago maryam.sabet • 0
0
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1
reply
402
views
GEOquery install problem
geoquery
3.2 years ago 261092095 ▴ 10
3
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5
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995
views
getGEO function doesn't download the expression data
geoquery
updated 3.2 years ago by ▴ 980 • written 3.2 years ago by ▴ 10
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4
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557
views
GEOquery using keywords in R
GEO geoquery geometadb
updated 3.3 years ago by 21k • written 3.3 years ago by ▴ 10
1
vote
4
replies
803
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 3.5 years ago by 21k • written 3.5 years ago by ▴ 10
1
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2
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589
views
Error when Creating Expression Set from Geo Set
geoquery
3.5 years ago dmm204 • 0
2
votes
2
replies
604
views
getGEO from GEOquery doesn't return probesets
geoquery getgeo probeset
updated 3.5 years ago by 58k • written 3.5 years ago by • 0
3
votes
2
replies
1.4k
views
getGEO error when trying to download a series matrix file
GEOquery getGEO
3.5 years ago rubi ▴ 90
2
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3
replies
543
views
GEO2R Gene Expression
geoquery
updated 3.5 years ago by 21k • written 3.5 years ago by ▴ 10
1
vote
1
reply
500
views
GEOquery: Diagnosing SOFT file error
geoquery geo data geo soft files
updated 3.5 years ago by 21k • written 3.5 years ago by ▴ 10
3
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4
replies
699
views
getGEO Error: Duplicate identifiers for rows
geoquery getgeo
updated 3.6 years ago by 21k • written 3.6 years ago by ▴ 10
1
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7
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678
views
model.matrix from GDS data
model.matrix lmFit eBayes GEOquery limma
3.6 years ago darthratus • 0
3
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11
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2.0k
views
GEOquery http:// url error
geoquery error getgeo microarray geo
updated 3.7 years ago by 21k • written 4.5 years ago by • 0
0
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1
reply
937
views
GEOquery getGEO 404
geoquery geoquery error message
updated 3.7 years ago by 21k • written 3.7 years ago by ▴ 20
3
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5
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2.1k
views
Tutorial: Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R GEO geoquery geoquery error message Tutorial
3.7 years ago martinguerrerog89 ▴ 20
10
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7
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1.1k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery summarizedexperiment GEO matrix
updated 3.7 years ago by 21k • written 3.7 years ago by ▴ 60
1
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3
replies
690
views
Boxplot and Identification of DEG
limma biobase geoquery
updated 3.8 years ago by ★ 27k • written 3.8 years ago by ▴ 30
3
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3
replies
676
views
How to construct an up-to-date and annotation-rich RangeSummarizedExperiment object around old microarray data?
geoquery summarizedexperiment rangedsummarizedexperiment
updated 3.9 years ago by 21k • written 3.9 years ago by ▴ 100
1
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3
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1.2k
views
Reading Illumina HT12 V4.0 Data from GEO into Lumi
lumi geoquery geo illumina human ht-12 v4 gene expression
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
0
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1
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741
views
GEOquery download error
geoquery error message GEOquery GSE GEO
4.1 years ago Barah ▴ 20
50 results • Page 1 of 1
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Comment: VST transformation and covariates in the TCGA TARGET GTEx dataset by Michael Love 34k
If this is taking too long, you can run it on a subsample (e.g. hundreds of samples) to identify parameters for the VST, and then apply it …
Comment: "full model matrix is less than full rank" by fernandogs97 • 0
Hello ATpoint, thank you very much for your fast and helpful response, finally I corrected the error by changing the separator, instead of …
Comment: unable to load shared object Rsamtools.dll': by Mike Smith ★ 5.1k
Can you include the command you're running (I guess it's `BiocManager::install("Rsamtools", type = "source")` )? It would also be useful to…
Comment: unable to load shared object Rsamtools.dll': by franck.richard • 0
Finally, I only encounter this problem with Rsamtools. It works fine with the other packages. Thank you for your help!
Comment: Unique GPos taking into account mcols by maltethodberg ▴ 140
Yes, I managed to find those functions via the VariantAnnotation package. The "Quad" versions are very handy for matching seqnames/pos/effe…
Votes
Answer: "full model matrix is less than full rank"
Comment: Unique GPos taking into account mcols
Comment: deseq2 machine sizing best practices for very large data set
Comment: Warning messages on Apple M1 BigSur
Answer: VST transformation and covariates in the TCGA TARGET GTEx dataset
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