Showing : geoquery • reset
0
votes
3
replies
286
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 27 days ago by 66k • written 28 days ago by • 0
0
votes
7
replies
459
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
8 weeks ago • updated 7 weeks ago needNGS • 0
0
votes
1
reply
505
views
Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
10 months ago Arianna • 0
0
votes
2
replies
716
views
Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 14 months ago by 50k • written 14 months ago by • 0
0
votes
2
replies
596
views
Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 14 months ago by • 0 • written 14 months ago by • 0
0
votes
1
reply
654
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 16 months ago by 66k • written 16 months ago by • 0
0
votes
1
reply
523
views
empty values when extracting beta values using the GEOquery
GSE61380 GEOquery
updated 18 months ago by ▴ 780 • written 18 months ago by • 0
3
votes
2
replies
1.4k
views
Unable to download supplementary files from GSE146963 using GEOquery
GEOquery
updated 21 months ago by 3.9k • written 21 months ago by ▴ 10
0
votes
1
reply
667
views
Regarding Installation of GEOquery
BiocManager installation GEOquery
updated 22 months ago by ▴ 780 • written 22 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
1.0k
views
How to get colData with GEOquery to prepare for DEseq2
GEOquery DEseq2
2.0 years ago Yugang • 0
1
vote
1
reply
2.5k
views
Error in downloading GEO Supplementary files
GEOquery
updated 2.2 years ago by ▴ 90 • written 2.2 years ago by • 0
5
votes
7
replies
2.2k
views
GEO series matrix empty
GEOquery GEO
2.3 years ago • updated 2.2 years ago gs.123 ▴ 20
3
votes
2
replies
1.2k
views
GEOquery returning NAs as probe names
GEOquery
updated 2.4 years ago by 21k • written 2.4 years ago by ▴ 30
3
votes
23
replies
3.9k
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery VROOM
2.5 years ago array chip ▴ 420
0
votes
1
reply
2.2k
views
Data frame with 0 columns and 0 rows
GEOquery
updated 2.5 years ago by ▴ 780 • written 2.5 years ago by • 0
1
vote
2
replies
2.4k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 2.5 years ago by 21k • written 2.5 years ago by ▴ 10
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 66k • 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 2.7 years ago by 66k • written 2.7 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 2.9 years ago by 21k • written 2.9 years ago by ▴ 10
0
votes
1
reply
877
views
GEOquery
GEOquery
updated 3.0 years ago by ▴ 780 • written 3.0 years ago by ▴ 10
6
votes
5
replies
1.3k
views
a problem of package ""
GEO GEOquery
updated 3.0 years ago by 16k • written 3.0 years ago by ▴ 20
2
votes
3
replies
1.0k
views
Problem about Geoquery
GEO GEOquery
3.0 years ago sheldon19931016 ▴ 20
3
votes
4
replies
1.4k
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
981
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray GSE22247 limma GEOquery IlluminaChip
updated 3.5 years ago by 50k • written 3.5 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 4.0 years ago by 21k • written 4.0 years ago by ▴ 40
1
vote
1
reply
1.1k
views
Table expression data from GEO file
GEO expression GEOquery
updated 4.1 years ago by ★ 3.3k • written 4.1 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 4.2 years ago by 66k • written 4.2 years ago by ▴ 830
0
votes
1
reply
1.0k
views
I have installed bioconductor, R still asks me to install it
bioconductor biocLite GEOquery package
updated 4.4 years ago by ★ 13k • written 4.4 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 4.6 years ago by 66k • written 4.6 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 4.6 years ago by 66k • written 4.6 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 4.9 years ago by 66k • written 4.9 years ago by • 0
0
votes
0
replies
964
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 5.1 years ago by 66k • written 5.1 years ago by ▴ 10
3
votes
6
replies
3.0k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
5.1 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 66k • written 5.1 years ago by • 0
2
votes
2
replies
2.1k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 5.5 years ago by 66k • written 5.5 years ago by ▴ 10
0
votes
2
replies
1.2k
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
5.5 years ago cschot3 • 0
0
votes
0
replies
964
views
Query based on PMIDs
SRAdb geoquery
5.5 years ago Deepak Tanwar ▴ 10
3
votes
4
replies
1.5k
views
GEOquery:Get error sampleNames
geoquery
updated 5.4 years ago by 0 • written 5.5 years ago by ▴ 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 5.8 years ago by 21k • written 5.8 years ago by ▴ 20
0
votes
1
reply
1.3k
views
question about getGEO function
geoquery
5.8 years ago maryam.sabet • 0
3
votes
2
replies
1.8k
views
Installing GEOQuery failed with conda
geoquery anaconda libxml2
updated 5.8 years ago by 25k • written 5.8 years ago by ▴ 10
0
votes
1
reply
889
views
GEOquery install problem
geoquery
5.8 years ago 261092095 ▴ 10
3
votes
5
replies
2.6k
views
getGEO function doesn't download the expression data
geoquery
updated 5.9 years ago by ★ 1.0k • written 5.9 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)? by ATpoint ★ 4.2k
I don't have an answer to the "why" but maybe a simple reimplemention will do: ```r seqs <- c("ATCATCGTATCAAAGTC", "AAAACGTATCAAAGTC", "TG…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by Guido Hooiveld ★ 4.0k
After checking `?DESeqDataSetFromMatrix` note this information: arguments provided to SummarizedExperiment including rowRanges and met…
Answer: Error in gseDO function by Guido Hooiveld ★ 4.0k
Yes, you are missing something. :-) For a GSEA you will need to use as input all genes that you are analyzing; these genes should be ran…
Comment: GSVA function by Robert Castelo ★ 3.3k
No, negative values may occur after log transformation when the `log(x)` is taken from a positive number `x with 0 < x < 1`, and therefore …
Comment: conumee with Infinium MethylationEPIC v2.0 by sgomez • 0
Hi Max, Could you try this? https://support.bioconductor.org/p/9136138/#9136840
Votes
A: Comparison between two different group's pathway analysis results
DiffBind Batch Effect
A: DiffBind Batch Effect
A: DiffBind Batch Effect
C: DiffBind Batch Effect
Awards • All
Popular Question to Robert Castelo ★ 3.3k
Popular Question to kevin.rue ▴ 350
Popular Question to Wei Shi ★ 3.6k
Popular Question to Gordon Smyth 50k
Popular Question to jovel_juan ▴ 30
Locations • All
Melbourne, Australia, 2 minutes ago
The city by the bay, 27 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
UPF, Barcelona, Spain, 1 hour ago
Germany, 1 hour ago
Traffic: 422 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6