Showing : GEOquery • reset
3
votes
2
replies
173
views
GEOquery returning NAs as probe names
GEOquery
updated 18 days ago by 21k • written 20 days ago by ▴ 30
3
votes
23
replies
632
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery VROOM
8 weeks ago array chip ▴ 410
1
vote
2
replies
216
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 8 weeks ago by 21k • written 9 weeks ago by ▴ 10
0
votes
1
reply
205
views
Data frame with 0 columns and 0 rows
GEOquery
updated 9 weeks ago by ▴ 160 • written 9 weeks ago by • 0
2
votes
3
replies
221
views
Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 10 weeks ago by 13k • written 10 weeks ago by ▴ 50
6
votes
7
replies
423
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 11 weeks ago by 58k • written 11 weeks ago by ▴ 50
1
vote
1
reply
352
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 4 months ago by 58k • written 4 months ago by ▴ 50
1
vote
1
reply
157
views
unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 6 months ago by 21k • written 6 months ago by ▴ 10
0
votes
1
reply
232
views
GEOquery
GEOquery
updated 8 months ago by ▴ 160 • written 8 months ago by • 0
6
votes
5
replies
376
views
a problem of package ""
GEO GEOquery
updated 8 months ago by 15k • written 8 months ago by ▴ 20
2
votes
3
replies
234
views
Problem about Geoquery
GEO GEOquery
8 months ago sheldon19931016 ▴ 20
7
votes
3
replies
3.7k
views
Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
6.7 years ago • updated 6 months ago Sean Davis 21k
0
votes
5
replies
1.6k
views
assayData: 0 features
geoquery
updated 11 months ago by • 0 • written 6.4 years ago by ▴ 230
3
votes
4
replies
490
views
when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery projectR
updated 12 months ago by 21k • written 12 months ago by ▴ 20
3
votes
1
reply
277
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray GSE22247 limma GEOquery IlluminaChip
updated 13 months ago by 44k • written 13 months ago by • 0
0
votes
2
replies
476
views
Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error GEOquery
updated 15 months ago by 1.5k • written 15 months ago by • 0
6
votes
3
replies
456
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 19 months ago by 21k • written 19 months ago by ▴ 40
1
vote
1
reply
238
views
Table expression data from GEO file
GEO expression GEOquery
updated 21 months ago by ★ 2.8k • written 21 months ago by • 0
4
votes
5
replies
416
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 22 months ago by 58k • written 22 months ago by ▴ 780
0
votes
1
reply
329
views
I have installed bioconductor, R still asks me to install it
bioconductor biocLite GEOquery package
updated 2.0 years ago by 13k • written 2.0 years ago by • 0
0
votes
3
replies
318
views
GEOquery and Feature data
GEOquery featureNames
updated 2.2 years ago by 21k • written 2.2 years ago by • 0
0
votes
3
replies
669
views
When applying rma to featureset get error: 'package' must be of length 1
oligo biobase GEOquery
updated 2.3 years ago by 58k • written 2.3 years ago by ▴ 20
2
votes
2
replies
830
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 2.3 years ago by 58k • written 2.3 years ago by ▴ 20
2
votes
1
reply
394
views
Downloading a private GEO with GEOquery
GEOquery
updated 2.3 years ago by 21k • written 2.3 years ago by ▴ 660
0
votes
5
replies
1.0k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 2.6 years ago by 58k • written 2.6 years ago by • 0
0
votes
0
replies
375
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 2.7 years ago by 58k • written 2.7 years ago by ▴ 10
3
votes
6
replies
1.4k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
2.8 years ago andy_shaps ▴ 10
1
vote
2
replies
511
views
How do I creat an expressionset if there is no GDS listed on the GEO database?
limma microarray GEOquery
updated 2.8 years ago by 58k • written 2.8 years ago by • 0
3
votes
4
replies
822
views
GEOquery:Get error sampleNames
geoquery
updated 3.0 years ago by 0 • written 3.2 years ago by ▴ 10
2
votes
2
replies
1.4k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 3.1 years ago by 58k • written 3.1 years ago by ▴ 10
0
votes
2
replies
579
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
3.2 years ago cschot3 • 0
0
votes
0
replies
444
views
Query based on PMIDs
SRAdb geoquery
3.2 years ago Deepak Tanwar ▴ 10
5
votes
12
replies
1.2k
views
Using eset while parsing GSE file located in a path
GEO geoquery
updated 3.4 years ago by 21k • written 3.4 years ago by ▴ 20
2
votes
3
replies
709
views
Filtering the probe set ids from GSE file
geoquery GSE
3.4 years ago mahm ▴ 20
3
votes
11
replies
1.1k
views
Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression geoquery GSE bioconductor microarray
updated 3.4 years ago by 21k • written 3.4 years ago by ▴ 20
3
votes
2
replies
833
views
Installing GEOQuery failed with conda
geoquery anaconda libxml2
updated 3.5 years ago by 25k • written 3.5 years ago by ▴ 10
0
votes
1
reply
723
views
question about getGEO function
geoquery
3.5 years ago maryam.sabet • 0
0
votes
1
reply
441
views
GEOquery install problem
geoquery
3.5 years ago 261092095 ▴ 10
3
votes
5
replies
1.2k
views
getGEO function doesn't download the expression data
geoquery
updated 3.5 years ago by ▴ 980 • written 3.5 years ago by ▴ 10
0
votes
4
replies
641
views
GEOquery using keywords in R
GEO geoquery geometadb
updated 3.7 years ago by 21k • written 3.7 years ago by ▴ 10
1
vote
4
replies
927
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 3.8 years ago by 21k • written 3.8 years ago by ▴ 10
1
vote
2
replies
654
views
Error when Creating Expression Set from Geo Set
geoquery
3.8 years ago dmm204 • 0
2
votes
2
replies
685
views
getGEO from GEOquery doesn't return probesets
geoquery getgeo probeset
updated 3.8 years ago by 58k • written 3.8 years ago by • 0
3
votes
2
replies
1.6k
views
getGEO error when trying to download a series matrix file
GEOquery getGEO
3.9 years ago rubi ▴ 100
2
votes
3
replies
639
views
GEO2R Gene Expression
geoquery
updated 3.9 years ago by 21k • written 3.9 years ago by ▴ 10
1
vote
1
reply
596
views
GEOquery: Diagnosing SOFT file error
geoquery geo data geo soft files
updated 3.9 years ago by 21k • written 3.9 years ago by ▴ 10
3
votes
4
replies
780
views
getGEO Error: Duplicate identifiers for rows
geoquery getgeo
updated 3.9 years ago by 21k • written 3.9 years ago by ▴ 10
1
vote
7
replies
778
views
model.matrix from GDS data
model.matrix lmFit eBayes GEOquery limma
3.9 years ago darthratus • 0
3
votes
11
replies
2.2k
views
GEOquery http:// url error
geoquery error getgeo microarray geo
updated 4.0 years ago by 21k • written 4.8 years ago by • 0
0
votes
1
reply
1.0k
views
GEOquery getGEO 404
geoquery geoquery error message
updated 4.0 years ago by 21k • written 4.0 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by swbarnes2 ▴ 970
You can have as many columns as you like in coldata, only those specified in the design will be used when you do the DESeq command So sur…
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Matthew • 0
Thanks for the suggestion, I'll give that a try! Based on the PCA, all three factors do tend to influence the results, so I'll try the colu…
Comment: fgsea not downloading due to new r version. Is there a way around this? by amir.khan • 0
Seems to have done the trick and worked. thanks!
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Michael Love 35k
Just to underscore swbarnes2 advice above, I'd also recommend discussing statistical design with a local statistician or someone familiar w…
Answer: Multi-factor paired RNAseq differential analysis with DEseq2 by swbarnes2 ▴ 970
First, I'd start by looking at all your samples in PCA. Does sex have a strong effect? Does it make sense to compare one tissue with anot…
Votes
Answer: fgsea not downloading due to new r version. Is there a way around this?
Comment: Unable to install Rhtslib in R-4.1.1
Answer: fgsea not downloading due to new r version. Is there a way around this?
Answer: Swish with more than two conditions. Add support for contrasts?
Answer: ERROR: unable to find an inherited method for function ‘dispersions<-’ for signa
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