Showing : GEOquery • reset
3
votes
23
replies
1.2k
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery VROOM
5 months ago array chip ▴ 420
2
votes
15
replies
7.9k
views
GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")
GEOquery GEOquery
updated 10.0 years ago by 59k • written 10.0 years ago by ★ 12k
5
votes
14
replies
10k
views
How to load GEO series matrix file in R Bioconductor
geoquery
updated 6.9 years ago by 21k • written 6.9 years ago by ▴ 10
2
votes
13
replies
1.8k
views
SCAN.UPC: exception thrown when loading GEOQuery
scan.upc geoquery rcurl
7.4 years ago lep ▴ 90
5
votes
12
replies
1.4k
views
Using eset while parsing GSE file located in a path
GEO geoquery
updated 3.7 years ago by 21k • written 3.7 years ago by ▴ 20
3
votes
11
replies
1.2k
views
Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression geoquery GSE bioconductor microarray
updated 3.7 years ago by 21k • written 3.7 years ago by ▴ 20
3
votes
11
replies
2.3k
views
GEOquery http:// url error
geoquery error getgeo microarray geo
updated 4.3 years ago by 21k • written 5.1 years ago by • 0
0
votes
8
replies
2.0k
views
GEOquery Error
GEOquery GEOquery
updated 10.3 years ago by 21k • written 10.3 years ago by ▴ 340
4
votes
8
replies
5.4k
views
getGEO - cannot Open URL issue
getGEO R GEOquery
6.6 years ago alptaciroglu ▴ 50
6
votes
7
replies
683
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 6 months ago by 59k • written 6 months ago by ▴ 50
1
vote
7
replies
832
views
model.matrix from GDS data
model.matrix lmFit eBayes GEOquery limma
4.3 years ago darthratus • 0
2
votes
7
replies
900
views
Not able to reproduce limma results from affy chip with or without CEL file from 2 GSE datasets
limma GEOquery affy
updated 5.2 years ago by 59k • written 5.2 years ago by • 0
0
votes
7
replies
2.4k
views
Normalizing Expressionset Exprs without Raw CEL files
geoquery normalization
updated 7.6 years ago by ▴ 580 • written 7.6 years ago by ▴ 20
0
votes
7
replies
1.8k
views
Getting annotation into eset
limma GEOquery limma GEOquery
updated 11.6 years ago by 21k • written 11.6 years ago by ▴ 120
10
votes
7
replies
1.4k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery summarizedexperiment GEO matrix
updated 4.4 years ago by 21k • written 4.4 years ago by ▴ 60
5
votes
7
replies
410
views
GEO series matrix empty
GEOquery GEO
3 months ago • updated 12 weeks ago gs.123 ▴ 20
2
votes
6
replies
7.8k
views
GEOquery: how to extract experimental data? (confused)
PROcess GEOquery PROcess GEOquery
updated 10.8 years ago by ▴ 60 • written 10.8 years ago by ★ 1.9k
0
votes
6
replies
1.2k
views
GEOquery and parsing SOFT files
GEOquery GEOquery
updated 13.0 years ago by 13k • written 13.0 years ago by ▴ 180
0
votes
6
replies
1.2k
views
Puma question
cdf GEOquery puma cdf GEOquery puma
11.6 years ago Manca Marco PATH ▴ 340
3
votes
6
replies
1.6k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
3.1 years ago andy_shaps ▴ 10
0
votes
6
replies
2.3k
views
processing Illumina HT12v4.0 expression data from GEO
Normalization affy PROcess GEOquery frma Normalization affy PROcess GEOquery frma
updated 7.8 years ago by 21k • written 7.9 years ago by ▴ 170
0
votes
6
replies
1.5k
views
GEOquery and GSE error
GEOquery GEOquery
updated 10.7 years ago by 21k • written 10.7 years ago by ▴ 760
0
votes
6
replies
882
views
installation error of a bioconductor package in my workspace
GEOquery GEOquery
updated 10.1 years ago by ▴ 680 • written 10.1 years ago by ★ 8.2k
0
votes
5
replies
1.1k
views
installation error of a bioconductor package in my workspace
GEOquery GEOquery
10.1 years ago carol white ▴ 680
0
votes
5
replies
1.3k
views
downloading different kinds of microarray data
Sequencing Microarray Genetics Annotation gpls convert GEOquery GEOmetadb Sequencing gpls
updated 11.8 years ago by ▴ 30 • written 11.8 years ago by 21k
0
votes
5
replies
1.2k
views
getGEO error
GEOquery GEOquery
updated 9.3 years ago by 21k • written 9.3 years ago by ▴ 440
3
votes
5
replies
2.8k
views
Tutorial: Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R GEO geoquery geoquery error message Tutorial
4.3 years ago martinguerrerog89 ▴ 20
2
votes
5
replies
903
views
Error with GEOquery
GEOquery GEOquery
updated 16.1 years ago by ▴ 170 • written 16.1 years ago by ▴ 480
3
votes
5
replies
1.3k
views
getGEO function doesn't download the expression data
geoquery
updated 3.9 years ago by ▴ 990 • written 3.9 years ago by ▴ 10
6
votes
5
replies
2.9k
views
Processing two-colour array data from GEO using limma when no raw data are available
limma geoquery
updated 6.3 years ago by 45k • written 6.3 years ago by ▴ 20
0
votes
5
replies
1.3k
views
XML package - 500 internal server error
GEOquery ArrayExpress GEOquery ArrayExpress
updated 9.1 years ago by 21k • written 9.1 years ago by ▴ 720
0
votes
5
replies
841
views
GEOquery and Sample Subsets
GEOquery GEOquery
updated 9.0 years ago by 21k • written 9.0 years ago by ▴ 750
4
votes
5
replies
490
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 2.2 years ago by 59k • written 2.2 years ago by ▴ 780
0
votes
5
replies
1.8k
views
assayData: 0 features
geoquery
updated 15 months ago by • 0 • written 6.7 years ago by ▴ 230
6
votes
5
replies
446
views
a problem of package ""
GEO GEOquery
updated 12 months ago by 15k • written 12 months ago by ▴ 20
0
votes
5
replies
1.1k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 2.9 years ago by 59k • written 2.9 years ago by • 0
1
vote
4
replies
1.0k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 4.1 years ago by 21k • written 4.1 years ago by ▴ 10
0
votes
4
replies
1.7k
views
GEOquery loading error
hgu133plus2 GEOquery BiocInstaller hgu133plus2 GEOquery BiocInstaller
updated 10.0 years ago by ★ 8.2k • written 10.0 years ago by ★ 12k
2
votes
4
replies
1.1k
views
GEOquery: Missing featureNames after creating expression set from series matrix file
geoquery
updated 7.0 years ago by 59k • written 7.0 years ago by ▴ 10
0
votes
4
replies
725
views
GEOquery using keywords in R
GEO geoquery geometadb
updated 4.0 years ago by 21k • written 4.0 years ago by ▴ 10
0
votes
4
replies
912
views
Agi4x44PreProcess
convert GEOquery Agi4x44PreProcess convert GEOquery Agi4x44PreProcess
updated 12.5 years ago by ▴ 460 • written 12.5 years ago by ★ 1.3k
0
votes
4
replies
1.4k
views
GEO and Limma
limma GEOquery limma GEOquery
10.6 years ago Voke AO ▴ 760
3
votes
4
replies
843
views
getGEO Error: Duplicate identifiers for rows
geoquery getgeo
updated 4.2 years ago by 21k • written 4.2 years ago by ▴ 10
0
votes
4
replies
911
views
error reading GSE file
GEOquery GEOquery
updated 7.4 years ago by • 0 • written 10.8 years ago by ▴ 570
0
votes
4
replies
788
views
stuck in biocLite("GEOquery")
GEOquery GEOquery
updated 11.2 years ago by ★ 8.2k • written 11.2 years ago by ▴ 420
5
votes
4
replies
2.9k
views
GEOquery Fails to Download Series Matrix File
geoquery ncbi geo geo data
5.5 years ago fongchunchan ▴ 30
0
votes
4
replies
1.3k
views
Meta data for gene from GEO
GEOquery GEOmetadb GEOquery GEOmetadb
updated 8.5 years ago by 21k • written 8.5 years ago by ★ 12k
0
votes
4
replies
3.7k
views
GEOquery
convert GEOquery convert GEOquery
updated 12.2 years ago by 21k • written 12.2 years ago by ★ 4.3k
2
votes
4
replies
1.0k
views
GEOquery: Shifted data columns in phenotype data
geoquery getgeo
6.3 years ago rfb • 0
0
votes
4
replies
1.4k
views
GSE normalization
limma GEOquery limma GEOquery
updated 14.9 years ago by ★ 1.2k • written 14.9 years ago by ▴ 100
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Comment: CPM after RUVseq by James W. MacDonald 59k
Also, you might be confused about something. CPM is counts/million counts, which *uses library size to scale normalize* and logCPM is just…
Comment: CPM after RUVseq by James W. MacDonald 59k
You shouldn't use CPM or logCPM for any of the steps! To use `RUVr` you need to fit a preliminary model using `edgeR`, which takes counts a…
Comment: CPM after RUVseq by Jess • 0
Thank you James! It hadn't occurred to me to input CPM rather than logCPM which is why my df$NormalizedCounts didn't exceed 17ish in valu…
Answer: RPX PXDataset error by Laurent Gatto 1.5k
- From the URL in the error, it looks like you have the latest (or a recent) `rpx` version. It is generally recommended to add the output o…
Answer: Package name already exists due to previous issue by shepherl 3.1k
This has been resolved. There needed to be a manual intervention by the core team to remove the old issue from the issue tracker database.…
Votes
Answer: CPM after RUVseq
Comment: Merging two plated in R
Answer: Merging two plated in R
Answer: Merging two plated in R
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
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