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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
James W. MacDonald
59k • written 10.0 years ago by
Guest User
★ 12k
5
votes
14
replies
10k
views
How to load GEO series matrix file in R Bioconductor
geoquery
updated 6.9 years ago by
Sean Davis
21k • written 6.9 years ago by
ayanava18
▴ 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
Sean Davis
21k • written 3.7 years ago by
mahm
▴ 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
Sean Davis
21k • written 3.7 years ago by
mahm
▴ 20
3
votes
11
replies
2.3k
views
GEOquery http:// url error
geoquery
error
getgeo
microarray
geo
updated 4.3 years ago by
Sean Davis
21k • written 5.1 years ago by
jblack29
• 0
0
votes
8
replies
2.0k
views
GEOquery Error
GEOquery
GEOquery
updated 10.3 years ago by
Sean Davis
21k • written 10.3 years ago by
ying chen
▴ 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
James W. MacDonald
59k • written 6 months ago by
Caitlin
▴ 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
James W. MacDonald
59k • written 5.2 years ago by
carine.genet
• 0
0
votes
7
replies
2.4k
views
Normalizing Expressionset Exprs without Raw CEL files
geoquery
normalization
updated 7.6 years ago by
Stephen Piccolo
▴ 580 • written 7.6 years ago by
PyPer
▴ 20
0
votes
7
replies
1.8k
views
Getting annotation into eset
limma
GEOquery
limma
GEOquery
updated 11.6 years ago by
Sean Davis
21k • written 11.6 years ago by
Timothy Wu
▴ 120
10
votes
7
replies
1.4k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery
summarizedexperiment
GEO
matrix
updated 4.4 years ago by
Sean Davis
21k • written 4.4 years ago by
rbronste
▴ 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
Dai, Hongying,
▴ 60 • written 10.8 years ago by
J.delasHeras@ed.ac.uk
★ 1.9k
0
votes
6
replies
1.2k
views
GEOquery and parsing SOFT files
GEOquery
GEOquery
updated 13.0 years ago by
Wolfgang Huber
13k • written 13.0 years ago by
Wacek Kusnierczyk
▴ 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
Sean Davis
21k • written 7.9 years ago by
Abhishek Pratap
▴ 170
0
votes
6
replies
1.5k
views
GEOquery and GSE error
GEOquery
GEOquery
updated 10.7 years ago by
Sean Davis
21k • written 10.7 years ago by
Voke AO
▴ 760
0
votes
6
replies
882
views
installation error of a bioconductor package in my workspace
GEOquery
GEOquery
updated 10.1 years ago by
carol white
▴ 680 • written 10.1 years ago by
Dan Tenenbaum
★ 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
Alex Levitchi
▴ 30 • written 11.8 years ago by
Sean Davis
21k
0
votes
5
replies
1.2k
views
getGEO error
GEOquery
GEOquery
updated 9.3 years ago by
Sean Davis
21k • written 9.3 years ago by
Alyaa Mahmoud
▴ 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
Peter
▴ 170 • written 16.1 years ago by
Sharon Anbu
▴ 480
3
votes
5
replies
1.3k
views
getGEO function doesn't download the expression data
geoquery
updated 3.9 years ago by
Axel Klenk
▴ 990 • written 3.9 years ago by
fwere
▴ 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
Gordon Smyth
45k • written 6.3 years ago by
Jason
▴ 20
0
votes
5
replies
1.3k
views
XML package - 500 internal server error
GEOquery
ArrayExpress
GEOquery
ArrayExpress
updated 9.1 years ago by
Sean Davis
21k • written 9.1 years ago by
Maciej Jończyk
▴ 720
0
votes
5
replies
841
views
GEOquery and Sample Subsets
GEOquery
GEOquery
updated 9.0 years ago by
Sean Davis
21k • written 9.0 years ago by
Thomas Hampton
▴ 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
James W. MacDonald
59k • written 2.2 years ago by
svlachavas
▴ 780
0
votes
5
replies
1.8k
views
assayData: 0 features
geoquery
updated 15 months ago by
H. Z. Amini
• 0 • written 6.7 years ago by
Ed Siefker
▴ 230
6
votes
5
replies
446
views
a problem of package ""
GEO
GEOquery
updated 12 months ago by
Hervé Pagès
15k • written 12 months ago by
sheldon19931016
▴ 20
0
votes
5
replies
1.1k
views
Install a custom CDF file
makecdf
RMA
annotation
biobase
GEOquery
updated 2.9 years ago by
James W. MacDonald
59k • written 2.9 years ago by
Seymoo
• 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
Sean Davis
21k • written 4.1 years ago by
arbet003
▴ 10
0
votes
4
replies
1.7k
views
GEOquery loading error
hgu133plus2
GEOquery
BiocInstaller
hgu133plus2
GEOquery
BiocInstaller
updated 10.0 years ago by
Dan Tenenbaum
★ 8.2k • written 10.0 years ago by
Guest User
★ 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
James W. MacDonald
59k • written 7.0 years ago by
knaxerova
▴ 10
0
votes
4
replies
725
views
GEOquery using keywords in R
GEO
geoquery
geometadb
updated 4.0 years ago by
Sean Davis
21k • written 4.0 years ago by
Didi
▴ 10
0
votes
4
replies
912
views
Agi4x44PreProcess
convert
GEOquery
Agi4x44PreProcess
convert
GEOquery
Agi4x44PreProcess
updated 12.5 years ago by
Neel Aluru
▴ 460 • written 12.5 years ago by
Francois Pepin
★ 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
Sean Davis
21k • written 4.2 years ago by
umahajan
▴ 10
0
votes
4
replies
911
views
error reading GSE file
GEOquery
GEOquery
updated 7.4 years ago by
acd13
• 0 • written 10.8 years ago by
Reema Singh
▴ 570
0
votes
4
replies
788
views
stuck in biocLite("GEOquery")
GEOquery
GEOquery
updated 11.2 years ago by
Dan Tenenbaum
★ 8.2k • written 11.2 years ago by
Jack Luo
▴ 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
Sean Davis
21k • written 8.5 years ago by
Guest User
★ 12k
0
votes
4
replies
3.7k
views
GEOquery
convert
GEOquery
convert
GEOquery
updated 12.2 years ago by
Sean Davis
21k • written 12.2 years ago by
Julie Zhu
★ 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
Weiwei Shi
★ 1.2k • written 14.9 years ago by
Steve Taylor
▴ 100
50 results • Page
1 of 1
Recent ...
Replies
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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