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Showing :
Geoquery
•
reset
0
votes
2
replies
82
views
How to get colData with GEOquery to prepare for DEseq2
GEOquery
DEseq2
8 days ago • updated 7 days ago
Yugang
• 0
0
votes
1
reply
110
views
Error in downloading GEO Supplementary files
GEOquery
updated 8 weeks ago by
tcalvo
▴ 70 • written 8 weeks ago by
wasilewska.karolina
• 0
5
votes
7
replies
393
views
GEO series matrix empty
GEOquery
GEO
12 weeks ago • updated 11 weeks ago
gs.123
▴ 20
3
votes
2
replies
291
views
GEOquery returning NAs as probe names
GEOquery
updated 4 months ago by
Sean Davis
21k • written 4 months ago by
John
▴ 30
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
1
vote
2
replies
445
views
GEO RNASeq data query
GEOquery
RNASeq
GEO
updated 5 months ago by
Sean Davis
21k • written 5 months ago by
20yx17
▴ 10
0
votes
1
reply
477
views
Data frame with 0 columns and 0 rows
GEOquery
updated 5 months ago by
Basti
▴ 280 • written 5 months ago by
墨
• 0
2
votes
3
replies
314
views
Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery
CancerData
limma
RCy3
CancerInSilico
updated 6 months ago by
Steve Lianoglou
13k • written 6 months ago by
Caitlin
▴ 50
6
votes
7
replies
668
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
1
reply
435
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray
GEOquery
cancerdata
MicroarrayData
updated 8 months ago by
James W. MacDonald
59k • written 8 months ago by
Caitlin
▴ 50
1
vote
1
reply
228
views
unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 10 months ago by
Sean Davis
21k • written 10 months ago by
pedram_torabian
▴ 10
0
votes
1
reply
298
views
GEOquery
GEOquery
updated 11 months ago by
Basti
▴ 280 • written 11 months ago by
curiousmind007
• 0
6
votes
5
replies
442
views
a problem of package ""
GEO
GEOquery
updated 11 months ago by
Hervé Pagès
15k • written 12 months ago by
sheldon19931016
▴ 20
2
votes
3
replies
295
views
Problem about Geoquery
GEO
GEOquery
12 months ago
sheldon19931016
▴ 20
7
votes
3
replies
4.0k
views
Tutorial:
Accessing Public Genomic Data from Bioconductor
geoquery
geometadb
sradb
Tutorial
7.0 years ago • updated 10 months ago
Sean Davis
21k
0
votes
5
replies
1.7k
views
assayData: 0 features
geoquery
updated 14 months ago by
H. Z. Amini
• 0 • written 6.7 years ago by
Ed Siefker
▴ 230
3
votes
4
replies
555
views
when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery
projectR
updated 15 months ago by
Sean Davis
21k • written 15 months ago by
jing
▴ 20
3
votes
1
reply
321
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray
GSE22247
limma
GEOquery
IlluminaChip
updated 17 months ago by
Gordon Smyth
45k • written 17 months ago by
bastien_chassagnol
• 0
0
votes
2
replies
586
views
Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error
GEOquery
updated 19 months ago by
Laurent Gatto
1.5k • written 19 months ago by
zhangzhuo77
• 0
6
votes
3
replies
531
views
GEOquery: preprocessing log of imported data
GEOquery
microarray
lumi
affy
limma
updated 23 months ago by
Sean Davis
21k • written 23 months ago by
fabian
▴ 40
1
vote
1
reply
315
views
Table expression data from GEO file
GEO
expression
GEOquery
updated 2.1 years ago by
Robert Castelo
★ 2.8k • written 2.1 years ago by
lsbew
• 0
4
votes
5
replies
488
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
1
reply
420
views
I have installed bioconductor, R still asks me to install it
bioconductor
biocLite
GEOquery
package
updated 2.3 years ago by
Steve Lianoglou
13k • written 2.3 years ago by
luhan.ni
• 0
0
votes
3
replies
359
views
GEOquery and Feature data
GEOquery
featureNames
updated 2.5 years ago by
Sean Davis
21k • written 2.5 years ago by
ekl
• 0
0
votes
3
replies
793
views
When applying rma to featureset get error: 'package' must be of length 1
oligo
biobase
GEOquery
updated 2.6 years ago by
James W. MacDonald
59k • written 2.6 years ago by
salamandra
▴ 20
2
votes
2
replies
994
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo
GEOquery
ExpressionSet
updated 2.6 years ago by
James W. MacDonald
59k • written 2.6 years ago by
salamandra
▴ 20
2
votes
1
reply
480
views
Downloading a private GEO with GEOquery
GEOquery
updated 2.6 years ago by
Sean Davis
21k • written 2.6 years ago by
Lluís Revilla Sancho
▴ 660
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
0
votes
0
replies
415
views
GEOquery: series matrix not parsing correctly
GEOquery
GEO
updated 3.0 years ago by
James W. MacDonald
59k • written 3.0 years ago by
andy_shaps
▴ 10
3
votes
6
replies
1.6k
views
GEOquery: HTTP error 403
GEOquery
GEO
HTTP error 403
3.1 years ago
andy_shaps
▴ 10
1
vote
2
replies
573
views
How do I creat an expressionset if there is no GDS listed on the GEO database?
limma
microarray
GEOquery
updated 3.1 years ago by
James W. MacDonald
59k • written 3.1 years ago by
pgurkirat
• 0
3
votes
4
replies
885
views
GEOquery:Get error sampleNames
geoquery
updated 3.4 years ago by
Bioconductor Community
0 • written 3.5 years ago by
ustcxyf
▴ 10
2
votes
2
replies
1.4k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 3.4 years ago by
James W. MacDonald
59k • written 3.4 years ago by
yurigorelik
▴ 10
0
votes
2
replies
629
views
GEOQuery bug, NCBI or package?
geoquery
ncbi geo
biobase
3.5 years ago
cschot3
• 0
0
votes
0
replies
486
views
Query based on PMIDs
SRAdb
geoquery
3.5 years ago
Deepak Tanwar
▴ 10
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
2
votes
3
replies
788
views
Filtering the probe set ids from GSE file
geoquery
GSE
3.7 years ago
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
2
replies
907
views
Installing GEOQuery failed with conda
geoquery
anaconda
libxml2
updated 3.8 years ago by
Martin Morgan
25k • written 3.8 years ago by
261092095
▴ 10
0
votes
1
reply
811
views
question about getGEO function
geoquery
3.8 years ago
maryam.sabet
• 0
0
votes
1
reply
471
views
GEOquery install problem
geoquery
3.8 years ago
261092095
▴ 10
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
0
votes
4
replies
721
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
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
1
vote
2
replies
693
views
Error when Creating Expression Set from Geo Set
geoquery
4.1 years ago
dmm204
• 0
2
votes
2
replies
747
views
getGEO from GEOquery doesn't return probesets
geoquery
getgeo
probeset
updated 4.2 years ago by
James W. MacDonald
59k • written 4.2 years ago by
dnedveck
• 0
3
votes
2
replies
1.8k
views
getGEO error when trying to download a series matrix file
GEOquery
getGEO
4.2 years ago
rubi
▴ 100
2
votes
3
replies
695
views
GEO2R Gene Expression
geoquery
updated 4.2 years ago by
Sean Davis
21k • written 4.2 years ago by
nkline
▴ 10
1
vote
1
reply
648
views
GEOquery: Diagnosing SOFT file error
geoquery
geo data
geo
soft files
updated 4.2 years ago by
Sean Davis
21k • written 4.2 years ago by
supermanrocketboy
▴ 10
3
votes
4
replies
842
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
50 results • Page
1 of 1
Recent ...
Replies
Answer: ashr vs apeglm for interaction data
by
Michael Love
36k
Can you show the MA plot for these two analyses? Also for a gene with a large LFC from ashr, can you show plotCounts?
Comment: Robust Multi-array Average could get negative value or not?
by
Yang Shi
• 0
Got the point sir~ Thanks so much!
Comment: Robust Multi-array Average could get negative value or not?
by
James W. MacDonald
59k
Because it's a small number.
Comment: Robust Multi-array Average could get negative value or not?
by
Yang Shi
• 0
Thanks for your quick reply sir! Could you tell me why 4 which you selected here?
Answer: Robust Multi-array Average could get negative value or not?
by
James W. MacDonald
59k
After running RMA, your data have been logged, base 2. Any value < 1 will have a negative value. Looking at the data from that GEO submissi…
Votes
Answer: Robust Multi-array Average could get negative value or not?
Answer: Robust Multi-array Average could get negative value or not?
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
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