Showing : geoquery • reset
0
votes
7
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318
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Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
19 days ago • updated 16 days ago needNGS • 0
0
votes
1
reply
452
views
Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
9 months ago Arianna • 0
0
votes
2
replies
666
views
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
votes
2
replies
560
views
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
votes
1
reply
613
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 14 months ago by 65k • written 14 months ago by • 0
8
votes
4
replies
4.7k
views
GEOquery: 0 features in the gset object
geoquery
updated 17 months ago by • 0 • written 8.7 years ago by ▴ 130
0
votes
1
reply
482
views
empty values when extracting beta values using the GEOquery
GSE61380 GEOquery
updated 17 months ago by ▴ 770 • written 17 months ago by • 0
7
votes
5
replies
6.0k
views
Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 8.9 years ago by 21k
3
votes
2
replies
1.3k
views
Unable to download supplementary files from GSE146963 using GEOquery
GEOquery
updated 20 months ago by 3.8k • written 20 months ago by ▴ 10
0
votes
1
reply
635
views
Regarding Installation of GEOquery
BiocManager installation GEOquery
updated 21 months ago by ▴ 770 • written 21 months ago by • 0
1
vote
5
replies
1.0k
views
Can't read in CEL files
GEO GEOquery
22 months ago OE • 0
0
votes
2
replies
948
views
How to get colData with GEOquery to prepare for DEseq2
GEOquery DEseq2
23 months ago Yugang • 0
1
vote
1
reply
2.4k
views
Error in downloading GEO Supplementary files
GEOquery
updated 2.1 years ago by ▴ 90 • written 2.1 years ago by • 0
5
votes
7
replies
2.1k
views
GEO series matrix empty
GEOquery GEO
2.2 years ago • updated 2.1 years ago gs.123 ▴ 20
3
votes
2
replies
1.2k
views
GEOquery returning NAs as probe names
GEOquery
updated 2.3 years ago by 21k • written 2.3 years ago by ▴ 30
3
votes
23
replies
3.8k
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery VROOM
2.4 years ago array chip ▴ 420
1
vote
2
replies
2.3k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 2.4 years ago by 21k • written 2.4 years ago by ▴ 10
0
votes
1
reply
2.1k
views
Data frame with 0 columns and 0 rows
GEOquery
updated 2.4 years ago by ▴ 770 • written 2.4 years ago by • 0
2
votes
3
replies
1.3k
views
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
votes
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
vote
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
vote
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
votes
1
reply
847
views
GEOquery
GEOquery
updated 2.9 years ago by ▴ 770 • written 2.9 years ago by ▴ 10
6
votes
5
replies
1.2k
views
a problem of package ""
GEO GEOquery
updated 2.9 years ago by 16k • written 2.9 years ago by ▴ 20
2
votes
3
replies
971
views
Problem about Geoquery
GEO GEOquery
2.9 years ago sheldon19931016 ▴ 20
0
votes
5
replies
3.4k
views
assayData: 0 features
geoquery
updated 3.1 years ago by ▴ 10 • written 8.6 years ago by ▴ 230
3
votes
4
replies
1.3k
views
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
932
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray GSE22247 limma GEOquery IlluminaChip
updated 3.4 years ago by 50k • written 3.4 years ago by • 0
0
votes
2
replies
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
votes
3
replies
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
vote
1
reply
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
replies
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
votes
1
reply
986
views
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
votes
3
replies
1.0k
views
GEOquery and Feature data
GEOquery featureNames
updated 4.4 years ago by 21k • written 4.4 years ago by • 0
0
votes
3
replies
1.7k
views
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
votes
2
replies
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
votes
1
reply
1.3k
views
Downloading a private GEO with GEOquery
GEOquery
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 730
0
votes
5
replies
2.0k
views
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
votes
0
replies
939
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 4.9 years ago by 65k • written 4.9 years ago by ▴ 10
3
votes
6
replies
2.9k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
5.0 years ago andy_shaps ▴ 10
1
vote
2
replies
1.3k
views
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
3
votes
4
replies
1.5k
views
GEOquery:Get error sampleNames
geoquery
updated 5.3 years ago by 0 • written 5.4 years ago by ▴ 10
2
votes
2
replies
2.0k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 5.4 years ago by 65k • written 5.4 years ago by ▴ 10
0
votes
2
replies
1.2k
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
5.4 years ago cschot3 • 0
0
votes
0
replies
931
views
Query based on PMIDs
SRAdb geoquery
5.4 years ago Deepak Tanwar ▴ 10
5
votes
12
replies
2.6k
views
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
votes
3
replies
1.6k
views
Filtering the probe set ids from GSE file
geoquery GSE
5.6 years ago mahm ▴ 20
3
votes
11
replies
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
3
votes
2
replies
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
votes
1
reply
1.3k
views
question about getGEO function
geoquery
5.7 years ago maryam.sabet • 0
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0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
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Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
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Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
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