Showing : GEOquery • reset
0
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159
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Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
9 weeks ago Arianna • 0
0
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2
replies
344
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
297
views
Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 6 months ago by • 0 • written 6 months ago by • 0
0
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1
reply
308
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
294
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
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2
replies
804
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
397
views
Regarding Installation of GEOquery
BiocManager installation GEOquery
updated 14 months ago by ▴ 720 • written 14 months ago by • 0
1
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5
replies
698
views
Can't read in CEL files
GEO GEOquery
15 months ago OE • 0
0
votes
2
replies
664
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
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7
replies
1.6k
views
GEO series matrix empty
GEOquery GEO
19 months ago gs.123 ▴ 20
3
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2
replies
845
views
GEOquery returning NAs as probe names
GEOquery
updated 20 months ago by 21k • written 20 months ago by ▴ 30
3
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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
888
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
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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
862
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
952
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
660
views
GEOquery
GEOquery
updated 2.3 years ago by ▴ 720 • written 2.3 years ago by ▴ 10
6
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5
replies
944
views
a problem of package ""
GEO GEOquery
updated 2.3 years ago by 16k • written 2.3 years ago by ▴ 20
2
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3
replies
718
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
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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
982
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
702
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
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1.4k
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
851
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
907
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
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1
reply
783
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
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796
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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
987
views
Downloading a private GEO with GEOquery
GEOquery
updated 4.0 years ago by 21k • written 4.0 years ago by ▴ 720
0
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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
769
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
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981
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
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2
replies
980
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
4.8 years ago cschot3 • 0
0
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0
replies
755
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
718
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
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Comment: DESeq2, results(dds, name = <reference>) interpretation results by Rockbar • 0
When I apply the model.matrix approach for getting the contrasts, the code > mod_mat <- model.matrix(design(dds), colData(dds)) > CondA.t…
Comment: DESeq2, results(dds, name = <reference>) interpretation results by Rockbar • 0
Yes, I agree, the correct contrast setting is quite challenging. The vignette says >contrast: a list of 2 character vectors: the names of…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
Advantage and disadvantage depends on the aim, what you plan to do with them (testing, plots, etc.). lengthScaledTPM puts back *in* the ge…
Comment: DESeq2, results(dds, name = <reference>) interpretation results by James W. MacDonald 63k
No, putting -1 in the design matrix is a cell means model, which is the opposite. If you used `~ Cond + Cond:Time`, you would specify a fac…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
Thank you for the response and apologies for my late reply. I think I´m starting getting the concept now. The hints with the cqn is quite …
Votes
Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Answer: Remove duplicates of colData in TreeSummarizedExperiment
Answer: Remove duplicates of colData in TreeSummarizedExperiment
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