Showing : GEOquery • reset
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Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
18 days ago • updated 15 days ago needNGS • 0
0
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1
reply
448
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Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
9 months ago Arianna • 0
0
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2
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662
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Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 12 months ago by 50k • written 12 months ago by • 0
0
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2
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559
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Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 12 months ago by • 0 • written 13 months ago by • 0
0
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1
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609
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Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 14 months ago by 65k • written 14 months ago by • 0
0
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1
reply
480
views
empty values when extracting beta values using the GEOquery
GSE61380 GEOquery
updated 17 months ago by ▴ 760 • written 17 months ago by • 0
3
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2
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1.3k
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Unable to download supplementary files from GSE146963 using GEOquery
GEOquery
updated 20 months ago by 3.8k • written 20 months ago by ▴ 10
0
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1
reply
629
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Regarding Installation of GEOquery
BiocManager installation GEOquery
updated 21 months ago by ▴ 760 • written 21 months ago by • 0
1
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5
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1.0k
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Can't read in CEL files
GEO GEOquery
22 months ago OE • 0
0
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2
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947
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How to get colData with GEOquery to prepare for DEseq2
GEOquery DEseq2
23 months ago Yugang • 0
1
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1
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2.4k
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Error in downloading GEO Supplementary files
GEOquery
updated 2.1 years ago by ▴ 90 • written 2.1 years ago by • 0
5
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7
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2.1k
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GEO series matrix empty
GEOquery GEO
2.2 years ago • updated 2.1 years ago gs.123 ▴ 20
3
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2
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1.2k
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GEOquery returning NAs as probe names
GEOquery
updated 2.3 years ago by 21k • written 2.3 years ago by ▴ 30
3
votes
23
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3.8k
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GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery VROOM
2.4 years ago array chip ▴ 420
0
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1
reply
2.1k
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Data frame with 0 columns and 0 rows
GEOquery
updated 2.4 years ago by ▴ 760 • written 2.4 years ago by • 0
1
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2
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2.3k
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GEO RNASeq data query
GEOquery RNASeq GEO
updated 2.4 years ago by 21k • written 2.4 years ago by ▴ 10
2
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3
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1.2k
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Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 2.4 years ago by ★ 13k • written 2.4 years ago by ▴ 50
6
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7
replies
2.1k
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 2.4 years ago by 65k • written 2.4 years ago by ▴ 50
1
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1
reply
1.1k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 2.6 years ago by 65k • written 2.6 years ago by ▴ 50
1
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1
reply
1.4k
views
unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 2.8 years ago by 21k • written 2.8 years ago by ▴ 10
0
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1
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845
views
GEOquery
GEOquery
updated 2.9 years ago by ▴ 760 • written 2.9 years ago by ▴ 10
6
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5
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1.2k
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a problem of package ""
GEO GEOquery
updated 2.9 years ago by 16k • written 2.9 years ago by ▴ 20
2
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3
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969
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Problem about Geoquery
GEO GEOquery
2.9 years ago sheldon19931016 ▴ 20
3
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4
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1.3k
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when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery projectR
updated 3.2 years ago by 21k • written 3.2 years ago by ▴ 20
3
votes
1
reply
931
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray GSE22247 limma GEOquery IlluminaChip
updated 3.3 years ago by 50k • written 3.3 years ago by • 0
0
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2
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1.8k
views
Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error GEOquery
updated 3.5 years ago by 1.6k • written 3.5 years ago by • 0
6
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3
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1.3k
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 3.9 years ago by 21k • written 3.9 years ago by ▴ 40
1
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1
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1.1k
views
Table expression data from GEO file
GEO expression GEOquery
updated 4.0 years ago by ★ 3.2k • written 4.0 years ago by • 0
5
votes
5
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1.2k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 4.1 years ago by 65k • written 4.1 years ago by ▴ 830
0
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1
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984
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I have installed bioconductor, R still asks me to install it
bioconductor biocLite GEOquery package
updated 4.3 years ago by ★ 13k • written 4.3 years ago by • 0
0
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3
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1.0k
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GEOquery and Feature data
GEOquery featureNames
updated 4.4 years ago by 21k • written 4.4 years ago by • 0
0
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3
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1.7k
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When applying rma to featureset get error: 'package' must be of length 1
oligo biobase GEOquery
updated 4.5 years ago by 65k • written 4.5 years ago by ▴ 20
3
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2
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2.2k
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 4.5 years ago by 65k • written 4.5 years ago by ▴ 20
2
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1
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1.3k
views
Downloading a private GEO with GEOquery
GEOquery
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 730
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5
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2.0k
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Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 4.8 years ago by 65k • written 4.8 years ago by • 0
0
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0
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938
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GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 4.9 years ago by 65k • written 4.9 years ago by ▴ 10
3
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6
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2.9k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
5.0 years ago andy_shaps ▴ 10
1
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2
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1.3k
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How do I creat an expressionset if there is no GDS listed on the GEO database?
limma microarray GEOquery
updated 5.0 years ago by 65k • written 5.0 years ago by • 0
2
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2
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2.0k
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geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 5.3 years ago by 65k • written 5.3 years ago by ▴ 10
0
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2
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1.2k
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
5.4 years ago cschot3 • 0
0
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0
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929
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Query based on PMIDs
SRAdb geoquery
5.4 years ago Deepak Tanwar ▴ 10
3
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4
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1.5k
views
GEOquery:Get error sampleNames
geoquery
updated 5.3 years ago by 0 • written 5.4 years ago by ▴ 10
5
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12
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2.6k
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Using eset while parsing GSE file located in a path
GEO geoquery
updated 5.6 years ago by 21k • written 5.6 years ago by ▴ 20
2
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3
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1.6k
views
Filtering the probe set ids from GSE file
geoquery GSE
5.6 years ago mahm ▴ 20
3
votes
11
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2.3k
views
Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression geoquery GSE bioconductor microarray
updated 5.6 years ago by 21k • written 5.6 years ago by ▴ 20
0
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1
reply
1.3k
views
question about getGEO function
geoquery
5.7 years ago maryam.sabet • 0
3
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2
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1.7k
views
Installing GEOQuery failed with conda
geoquery anaconda libxml2
updated 5.7 years ago by 25k • written 5.7 years ago by ▴ 10
0
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1
reply
866
views
GEOquery install problem
geoquery
5.7 years ago 261092095 ▴ 10
3
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5
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2.5k
views
getGEO function doesn't download the expression data
geoquery
updated 5.8 years ago by ★ 1.0k • written 5.8 years ago by ▴ 10
0
votes
4
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1.5k
views
GEOquery using keywords in R
GEO geoquery geometadb
updated 5.9 years ago by 21k • written 5.9 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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