Showing : geoquery • reset
5
votes
12
replies
3.4k
views
Using eset while parsing GSE file located in a path
GEO geoquery
updated 7.0 years ago by 21k • written 7.0 years ago by ▴ 20
2
votes
3
replies
2.2k
views
Filtering the probe set ids from GSE file
geoquery GSE
7.1 years ago mahm ▴ 20
3
votes
11
replies
3.4k
views
Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression geoquery GSE bioconductor microarray
updated 7.1 years ago by 21k • written 7.1 years ago by ▴ 20
3
votes
2
replies
2.3k
views
Installing GEOQuery failed with conda
geoquery anaconda libxml2
updated 7.1 years ago by 25k • written 7.1 years ago by ▴ 10
0
votes
1
reply
1.6k
views
question about getGEO function
geoquery
7.1 years ago maryam.sabet • 0
0
votes
1
reply
1.1k
views
GEOquery install problem
geoquery
7.2 years ago 261092095 ▴ 10
3
votes
5
replies
3.5k
views
getGEO function doesn't download the expression data
geoquery
updated 7.2 years ago by ★ 1.1k • written 7.2 years ago by ▴ 10
0
votes
4
replies
2.0k
views
GEOquery using keywords in R
GEO geoquery geometadb
updated 7.3 years ago by 21k • written 7.3 years ago by ▴ 10
1
vote
4
replies
2.9k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 7.4 years ago by 21k • written 7.4 years ago by ▴ 10
1
vote
2
replies
1.5k
views
Error when Creating Expression Set from Geo Set
geoquery
7.5 years ago dmm204 • 0
2
votes
2
replies
1.5k
views
getGEO from GEOquery doesn't return probesets
geoquery getgeo probeset
updated 7.5 years ago by 68k • written 7.5 years ago by • 0
3
votes
2
replies
4.6k
views
getGEO error when trying to download a series matrix file
GEOquery getGEO
7.5 years ago rubi ▴ 110
2
votes
3
replies
1.9k
views
GEO2R Gene Expression
geoquery
updated 7.5 years ago by 21k • written 7.5 years ago by ▴ 10
1
vote
1
reply
1.8k
views
GEOquery: Diagnosing SOFT file error
geoquery geo data geo soft files
updated 7.5 years ago by 21k • written 7.5 years ago by ▴ 10
3
votes
4
replies
1.7k
views
getGEO Error: Duplicate identifiers for rows
geoquery getgeo
updated 7.6 years ago by 21k • written 7.6 years ago by ▴ 10
1
vote
7
replies
2.2k
views
model.matrix from GDS data
model.matrix lmFit eBayes GEOquery limma
7.6 years ago darthratus • 0
3
votes
11
replies
5.3k
views
GEOquery http:// url error
geoquery error getgeo microarray geo
updated 7.7 years ago by 21k • written 8.4 years ago by • 0
0
votes
1
reply
2.0k
views
GEOquery getGEO 404
geoquery geoquery error message
updated 7.7 years ago by 21k • written 7.7 years ago by ▴ 20
3
votes
5
replies
6.4k
views
Tutorial: Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R GEO geoquery geoquery error message Tutorial
7.7 years ago martinguerrerog89 ▴ 20
10
votes
7
replies
3.2k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery summarizedexperiment GEO matrix
updated 7.7 years ago by 21k • written 7.7 years ago by ▴ 60
1
vote
3
replies
2.0k
views
Boxplot and Identification of DEG
limma biobase geoquery
updated 7.8 years ago by ★ 29k • written 7.8 years ago by ▴ 30
3
votes
3
replies
2.0k
views
How to construct an up-to-date and annotation-rich RangeSummarizedExperiment object around old microarray data?
geoquery summarizedexperiment rangedsummarizedexperiment
updated 7.9 years ago by 21k • written 7.9 years ago by ▴ 100
1
vote
3
replies
3.0k
views
Reading Illumina HT12 V4.0 Data from GEO into Lumi
lumi geoquery geo illumina human ht-12 v4 gene expression
updated 7.9 years ago by 53k • written 7.9 years ago by • 0
0
votes
1
reply
2.0k
views
GEOquery download error
geoquery error message GEOquery GSE GEO
8.0 years ago Barah ▴ 20
3
votes
3
replies
8.6k
views
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq rna-seq limma geoquery edger
updated 8.1 years ago by 21k • written 8.1 years ago by ▴ 20
2
votes
3
replies
2.3k
views
GEOquery problem in calling the function in Rstudio
R software error biobase geoquery
updated 8.2 years ago by 68k • written 8.2 years ago by • 0
0
votes
0
replies
1.0k
views
MILES dataset download
software error geoquery
updated 8.2 years ago by 4.2k • written 8.2 years ago by • 0
0
votes
1
reply
850
views
Finding all samples with specific gene
geo2r lima geoquery
updated 8.3 years ago by 68k • written 8.3 years ago by • 0
0
votes
2
replies
2.1k
views
Error in GEOquery
geoquery getgeo R
updated 8.4 years ago by 68k • written 8.4 years ago by • 0
2
votes
2
replies
2.0k
views
Problem with GEOquery R package in Windows when trying to download specific GEO processed data
geoquery affymetrix microarrays windows8 getGEO
updated 8.4 years ago by 21k • written 8.4 years ago by ▴ 840
2
votes
7
replies
1.9k
views
Not able to reproduce limma results from affy chip with or without CEL file from 2 GSE datasets
limma GEOquery affy
updated 8.5 years ago by 68k • written 8.5 years ago by • 0
1
vote
2
replies
1.4k
views
How to compare 10 GSMxxxxx from one GSE to 10 GSM from another GSE with GEOQuery
geoquery
updated 8.5 years ago by 68k • written 8.5 years ago by • 0
1
vote
1
reply
1.2k
views
NA's returned for GEO GPL3921 platform probsets
geoquery
9.1 years ago • updated 8.6 years ago Zach Roe ▴ 10
1
vote
2
replies
1.4k
views
Error in "getGSEDataTables" in GSEquery package
geoquery
updated 8.7 years ago by 21k • written 9.5 years ago by ▴ 10
0
votes
0
replies
1.6k
views
getGEO: not all columns named in 'colClasses' exist and invalid 'nlines' argument
GEOquery
8.8 years ago Shicheng Guo • 0
2
votes
2
replies
3.0k
views
GEOquery error in downloading SOFT files
geoquery getgeo GEO
8.8 years ago hzc363 ▴ 20
6
votes
4
replies
5.7k
views
GEOquery Fails to Download Series Matrix File
geoquery ncbi geo geo data
8.8 years ago fongchunchan ▴ 30
1
vote
3
replies
2.7k
views
Log-Transform Values of eSet
expressionset bioconductor limma geoquery
updated 8.9 years ago by ▴ 840 • written 8.9 years ago by • 0
1
vote
1
reply
2.6k
views
GEO error : Warning message: In read.table(file = file, header = header, sep = sep, quote = quote, : not all columns named in 'colClasses' exist
geoquery geoquery error message
updated 9.1 years ago by 21k • written 9.1 years ago by ▴ 10
0
votes
0
replies
1.1k
views
GEOQuery - Encoding UTF-8
geoquery UTF
9.1 years ago Adrian Johnson ▴ 330
0
votes
1
reply
1000
views
Iteration through a list failing
geoquery
updated 9.3 years ago by 68k • written 9.3 years ago by • 0
2
votes
1
reply
2.2k
views
GEOquery::getGEO warning: not all columns named in 'colClasses' exist
GEOquery
updated 9.3 years ago by 21k • written 9.3 years ago by ▴ 110
4
votes
3
replies
3.4k
views
Modifying eset@assayData$exprs : Error : cannot change value of locked binding for 'exprs'
GEOquery
updated 9.4 years ago by ★ 13k • written 9.4 years ago by ▴ 40
6
votes
1
reply
2.0k
views
select negative control probes with GEOquery
GEOquery MBCB limma
9.6 years ago goldberg.jm ▴ 10
6
votes
5
replies
4.3k
views
Processing two-colour array data from GEO using limma when no raw data are available
limma geoquery
updated 9.6 years ago by 53k • written 9.6 years ago by ▴ 20
2
votes
4
replies
2.0k
views
GEOquery: Shifted data columns in phenotype data
geoquery getgeo
9.7 years ago rfb • 0
2
votes
2
replies
2.2k
views
getGEO error
getgeo geoquery
updated 9.7 years ago by 53k • written 9.7 years ago by ▴ 10
1
vote
1
reply
2.0k
views
Error of GDS2eSet() function
convert geoquery error GDS2eSet
updated 9.7 years ago by 68k • written 9.7 years ago by • 0
0
votes
1
reply
1.6k
views
Getting data from GEO
affymetrix microarrays GEO geoquery
updated 9.8 years ago by 68k • written 9.8 years ago by • 0
1
vote
1
reply
848
views
Problem with GDS2eSet(). How can I edit GDS column name so it matches GPL?
geoquery
updated 9.9 years ago by 21k • written 9.9 years ago by ▴ 10
241 results • Page 2 of 5
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Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by James W. MacDonald 68k
It may not be that common for bulk RNA-Seq, but in my experience it's very common for bulk miRNA-Seq.
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Nice. That's great to hear. `sva` was actually the next step I was planning to try. My colleagues haven't seen this kind of pattern before …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by James W. MacDonald 68k
It is not uncommon for library size to be apparent in an MDS plot. You can use `sva` or `RUV` to account for that.
Comment: p-adjusted values in multiple comparisons by Josh • 0
Yes, using lmFit with block and duplicateCorrelation is appropriate; mobile data collection can illustrate blocking importance. First estim…
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Understood, thanks. The issue I'm seeing is that even after normalization, the MDSplot still orders samples by library size. I suspect cell…
Votes
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: How to construct a BSgenome object from a custom genome assembly using BSgenomeF
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