Showing : geoquery • reset
0
votes
3
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242
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 6 days ago by 65k • written 7 days ago by • 0
0
votes
7
replies
405
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
5 weeks ago • updated 4 weeks ago needNGS • 0
0
votes
1
reply
478
views
Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
9 months ago Arianna • 0
0
votes
2
replies
690
views
Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 13 months ago by 50k • written 13 months ago by • 0
0
votes
2
replies
582
views
Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 13 months ago by • 0 • written 13 months ago by • 0
0
votes
1
reply
635
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 15 months ago by 65k • written 15 months ago by • 0
0
votes
1
reply
507
views
empty values when extracting beta values using the GEOquery
GSE61380 GEOquery
updated 17 months ago by ▴ 780 • written 17 months ago by • 0
3
votes
2
replies
1.4k
views
Unable to download supplementary files from GSE146963 using GEOquery
GEOquery
updated 20 months ago by 3.9k • written 20 months ago by ▴ 10
0
votes
1
reply
654
views
Regarding Installation of GEOquery
BiocManager installation GEOquery
updated 21 months ago by ▴ 780 • written 21 months ago by • 0
1
vote
5
replies
1.1k
views
Can't read in CEL files
GEO GEOquery
23 months ago OE • 0
0
votes
2
replies
979
views
How to get colData with GEOquery to prepare for DEseq2
GEOquery DEseq2
24 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 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
2.4k
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
2.2k
views
Data frame with 0 columns and 0 rows
GEOquery
updated 2.4 years ago by ▴ 780 • 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 2.5 years ago by ★ 13k • written 2.5 years ago by ▴ 50
6
votes
7
replies
2.2k
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 2.5 years ago by 65k • written 2.5 years ago by ▴ 50
1
vote
1
reply
1.2k
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
1.5k
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
865
views
GEOquery
GEOquery
updated 2.9 years ago by ▴ 780 • written 2.9 years ago by ▴ 10
6
votes
5
replies
1.3k
views
a problem of package ""
GEO GEOquery
updated 2.9 years ago by 16k • written 3.0 years ago by ▴ 20
2
votes
3
replies
993
views
Problem about Geoquery
GEO GEOquery
3.0 years ago sheldon19931016 ▴ 20
7
votes
5
replies
6.1k
views
Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 8.9 years ago by 21k
0
votes
5
replies
3.5k
views
assayData: 0 features
geoquery
updated 3.2 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 3.3 years ago by 21k • written 3.3 years ago by ▴ 20
3
votes
1
reply
962
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 3.6 years ago by 1.6k • written 3.6 years ago by • 0
6
votes
3
replies
1.4k
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 ★ 3.3k • 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
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1
reply
1.0k
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
1.1k
views
GEOquery and Feature data
GEOquery featureNames
updated 4.5 years ago by 21k • written 4.5 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
2.3k
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 4.6 years ago by 21k • written 4.6 years ago by ▴ 730
0
votes
5
replies
2.1k
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
956
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 5.0 years ago by 65k • written 5.0 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 5.1 years ago by 65k • written 5.1 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
2.1k
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
951
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 5.7 years ago by 21k • written 5.7 years ago by ▴ 20
2
votes
3
replies
1.7k
views
Filtering the probe set ids from GSE file
geoquery GSE
5.7 years ago mahm ▴ 20
3
votes
11
replies
2.4k
views
Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression geoquery GSE bioconductor microarray
updated 5.7 years ago by 21k • written 5.7 years ago by ▴ 20
3
votes
2
replies
1.8k
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
50 results • Page 1 of 1
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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