Showing : geoquery • reset
0
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80
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Regarding Installation of GEOquery
BiocManager installation GEOquery
updated 16 days ago by ▴ 390 • written 16 days ago by • 0
1
vote
5
replies
187
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Can't read in CEL files
GEO GEOquery
7 weeks ago OE • 0
0
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2
replies
162
views
How to get colData with GEOquery to prepare for DEseq2
GEOquery DEseq2
3 months ago Yugang • 0
0
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1
reply
199
views
Error in downloading GEO Supplementary files
GEOquery
updated 4 months ago by ▴ 70 • written 4 months ago by • 0
5
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7
replies
552
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GEO series matrix empty
GEOquery GEO
5 months ago gs.123 ▴ 20
3
votes
2
replies
370
views
GEOquery returning NAs as probe names
GEOquery
updated 7 months ago by 21k • written 7 months ago by ▴ 30
3
votes
23
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1.4k
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery VROOM
8 months ago array chip ▴ 420
1
vote
2
replies
584
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 8 months ago by 21k • written 8 months ago by ▴ 10
0
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1
reply
668
views
Data frame with 0 columns and 0 rows
GEOquery
updated 8 months ago by ▴ 390 • written 8 months ago by • 0
2
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3
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383
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Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 8 months ago by 13k • written 9 months ago by ▴ 50
6
votes
7
replies
827
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 9 months ago by 60k • written 9 months ago by ▴ 50
1
vote
1
reply
500
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 11 months ago by 60k • written 11 months ago by ▴ 50
1
vote
1
reply
301
views
unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 13 months ago by 21k • written 13 months ago by ▴ 10
0
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1
reply
349
views
GEOquery
GEOquery
updated 14 months ago by ▴ 390 • written 14 months ago by • 0
6
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5
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510
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a problem of package ""
GEO GEOquery
updated 14 months ago by 15k • written 14 months ago by ▴ 20
2
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3
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342
views
Problem about Geoquery
GEO GEOquery
14 months ago sheldon19931016 ▴ 20
7
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4
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4.2k
views
Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
updated 8 weeks ago by • 0 • written 7.2 years ago by 21k
0
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5
replies
1.9k
views
assayData: 0 features
geoquery
updated 17 months ago by • 0 • written 6.9 years ago by ▴ 230
3
votes
4
replies
620
views
when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery projectR
updated 18 months ago by 21k • written 18 months ago by ▴ 20
3
votes
1
reply
359
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray GSE22247 limma GEOquery IlluminaChip
updated 20 months ago by 46k • written 20 months ago by • 0
0
votes
2
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664
views
Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error GEOquery
updated 22 months ago by 1.5k • written 22 months ago by • 0
6
votes
3
replies
612
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 2.2 years ago by 21k • written 2.2 years ago by ▴ 40
1
vote
1
reply
404
views
Table expression data from GEO file
GEO expression GEOquery
updated 2.3 years ago by ★ 2.9k • written 2.3 years ago by • 0
5
votes
5
replies
553
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 2.4 years ago by 60k • written 2.4 years ago by ▴ 800
0
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1
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470
views
I have installed bioconductor, R still asks me to install it
bioconductor biocLite GEOquery package
updated 2.6 years ago by 13k • written 2.6 years ago by • 0
0
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3
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408
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GEOquery and Feature data
GEOquery featureNames
updated 2.7 years ago by 21k • written 2.7 years ago by • 0
0
votes
3
replies
866
views
When applying rma to featureset get error: 'package' must be of length 1
oligo biobase GEOquery
updated 2.8 years ago by 60k • written 2.8 years ago by ▴ 20
2
votes
2
replies
1.1k
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 2.8 years ago by 60k • written 2.8 years ago by ▴ 20
2
votes
1
reply
559
views
Downloading a private GEO with GEOquery
GEOquery
updated 2.8 years ago by 21k • written 2.8 years ago by ▴ 690
0
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5
replies
1.2k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 3.1 years ago by 60k • written 3.1 years ago by • 0
0
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0
replies
450
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 3.3 years ago by 60k • written 3.3 years ago by ▴ 10
3
votes
6
replies
1.7k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
3.3 years ago andy_shaps ▴ 10
1
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2
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617
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How do I creat an expressionset if there is no GDS listed on the GEO database?
limma microarray GEOquery
updated 3.3 years ago by 60k • written 3.3 years ago by • 0
3
votes
4
replies
937
views
GEOquery:Get error sampleNames
geoquery
updated 3.6 years ago by 0 • written 3.7 years ago by ▴ 10
2
votes
2
replies
1.5k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 3.7 years ago by 60k • written 3.7 years ago by ▴ 10
0
votes
2
replies
669
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
3.7 years ago cschot3 • 0
0
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0
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532
views
Query based on PMIDs
SRAdb geoquery
3.7 years ago Deepak Tanwar ▴ 10
5
votes
12
replies
1.5k
views
Using eset while parsing GSE file located in a path
GEO geoquery
updated 3.9 years ago by 21k • written 3.9 years ago by ▴ 20
2
votes
3
replies
865
views
Filtering the probe set ids from GSE file
geoquery GSE
3.9 years ago mahm ▴ 20
3
votes
11
replies
1.3k
views
Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression geoquery GSE bioconductor microarray
updated 4.0 years ago by 21k • written 4.0 years ago by ▴ 20
3
votes
2
replies
1.0k
views
Installing GEOQuery failed with conda
geoquery anaconda libxml2
updated 4.0 years ago by 25k • written 4.0 years ago by ▴ 10
0
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1
reply
849
views
question about getGEO function
geoquery
4.0 years ago maryam.sabet • 0
0
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1
reply
497
views
GEOquery install problem
geoquery
4.0 years ago 261092095 ▴ 10
3
votes
5
replies
1.4k
views
getGEO function doesn't download the expression data
geoquery
updated 4.1 years ago by ▴ 990 • written 4.1 years ago by ▴ 10
0
votes
4
replies
777
views
GEOquery using keywords in R
GEO geoquery geometadb
updated 4.2 years ago by 21k • written 4.2 years ago by ▴ 10
1
vote
4
replies
1.1k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 4.3 years ago by 21k • written 4.3 years ago by ▴ 10
1
vote
2
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722
views
Error when Creating Expression Set from Geo Set
geoquery
4.4 years ago dmm204 • 0
2
votes
2
replies
801
views
getGEO from GEOquery doesn't return probesets
geoquery getgeo probeset
updated 4.4 years ago by 60k • written 4.4 years ago by • 0
3
votes
2
replies
2.0k
views
getGEO error when trying to download a series matrix file
GEOquery getGEO
4.4 years ago rubi ▴ 100
2
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3
replies
744
views
GEO2R Gene Expression
geoquery
updated 4.4 years ago by 21k • written 4.4 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: OPLS-DA: confidence interval for accuracy metric by etienne.thevenot ▴ 20
- The bootstrapping approach can be used to compute the CIs: see here for an example: Mendez et al. (2019). « A comparative evaluation …
Comment: Data input for aracne2regulon function in viper package by xlal • 0
You are right!And may be we should check the gene symbols cause when I open the expression matrix in EXCEL,it will change some genes into m…
Comment: unable to install.packages("spatialLIBD") by Leonardo Collado Torres ▴ 1000
All the solutions Lori proposed are valid. The `STexampleData` package I think has only 1 of our samples (see https://bioconductor.org/pack…
Answer: how to use Rsamtools to parse extra fields from STAR alignment by Martin Morgan 25k
The 'extra columns' are called 'tags' in the SAM specification. Following the documentation `?ScanBamParam` you should add `tag = "NH"`. Se…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip by Delta._.43 ▴ 10
Yes, indeed it is the same error. Here are the first few lines of my count file. ``` "ENSG00000000003":"001" 0 "ENSG00000000003":"002" 1032…
Votes
Answer: spot- vs cell-level data access
Answer: unable to install.packages("spatialLIBD")
Comment: unable to install.packages("spatialLIBD")
error running UniProt.ws
Answer: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
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