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Showing :
Expressionset
•
reset
2
votes
5
replies
3.9k
views
GSVA error - incomplete instalation?
GSVA
ExpressionSet
8.4 years ago
thrabe
• 0
6
votes
7
replies
3.7k
views
GOexpress: use DESeq2 data object as input
GOexpress
deseq2
expressionset
8.5 years ago
martin.hoelzer
▴ 20
2
votes
1
reply
3.1k
views
ExpressionSet: Remove NA values above a certain threshold
expressionset
updated 8.7 years ago by
Aaron Lun
★ 28k • written 8.7 years ago by
philipp24
▴ 30
1
vote
2
replies
3.0k
views
how to update feature data with different dimensions in expressionSet?
biobase
eSet
expressionSet
updated 7.5 years ago by
Martin Morgan
25k • written 7.5 years ago by
Guido Hooiveld
★ 3.9k
0
votes
3
replies
2.5k
views
Annotation in ExpressionSet object
ExpressionSet
globaltest
7.9 years ago
NS
▴ 60
3
votes
10
replies
2.3k
views
Question about converting rownames of an expression dataset to their corresponding gene symbols
filtering
bioconductor
genesymbols
expressionset
9.1 years ago
svlachavas
▴ 830
3
votes
2
replies
2.3k
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo
GEOquery
ExpressionSet
updated 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
salamandra
▴ 20
4
votes
8
replies
2.2k
views
Help! ExpressionSet function from Biobase not working! (issue with data structure??)
limma
biobase
ExpressionSet
updated 4.0 years ago by
Gordon Smyth
50k • written 4.0 years ago by
sa825
• 0
1
vote
3
replies
2.2k
views
Log-Transform Values of eSet
expressionset
bioconductor
limma
geoquery
updated 7.5 years ago by
svlachavas
▴ 830 • written 7.5 years ago by
bi_Scholar
• 0
0
votes
3
replies
2.1k
views
[ExpressionSet] Question: Error in validObject(.Object)
ExpressionSet
Assay
NanoString
Error
Data
updated 21 months ago by
James W. MacDonald
65k • written 21 months ago by
junli1988
• 0
2
votes
4
replies
1.9k
views
Weird error after trying to subset an microarray expression set with gene symbols from topTable function from limma
expressionset
limma
annotation
affymetrix microarrays
updated 8.2 years ago by
Martin Morgan
25k • written 8.2 years ago by
svlachavas
▴ 830
3
votes
3
replies
1.8k
views
Error running CellMix SampleAnalysis vignette
software error
cellmix
vignette
expressionset
7.3 years ago
gabor.halasz
• 0
1
vote
10
replies
1.8k
views
Error when restore rownames of Feature data of ExpressionSet
expressionset
updated 6.6 years ago by
Martin Morgan
25k • written 6.6 years ago by
peirinl
• 0
3
votes
5
replies
1.6k
views
Get Gen-Expression values accross samples for ONE Gene given by Gene-Symbol
expressionset
bioconductor
updated 7.6 years ago by
polemiraza
▴ 70 • written 7.6 years ago by
bi_Scholar
• 0
0
votes
6
replies
1.5k
views
expression correlation on an ExpressionSet
ExpressionSet
caseControl
Correlation
Plot
updated 6.9 years ago by
vulegom
• 0 • written 7.2 years ago by
DataFanatic
▴ 10
5
votes
7
replies
1.5k
views
Difficulty extending ExpressionSet
biobase
expressionset
eset
updated 5.7 years ago by
Martin Morgan
25k • written 5.7 years ago by
andrew.birnberg
▴ 20
3
votes
9
replies
1.4k
views
How many features an ExpressionSet can contain ?
ExpressionSet
22 months ago
OE
• 0
1
vote
2
replies
1.4k
views
How can I see that my samples is normalized or not?
Normalization
ExpressionSet
Series
updated 8.1 years ago by
James W. MacDonald
65k • written 8.1 years ago by
vahideh
• 0
0
votes
1
reply
1.4k
views
InSilicoMerging error when using merge
insilicomerging
error
insilicodb
expressionset
7.2 years ago
andreas.pittroff
• 0
0
votes
0
replies
1.3k
views
Export expressionSet to ArrayExpress "processed data"
expressionset
simpleaffy
arrayexpress
tsv
7.7 years ago
Steffen Neumann
▴ 30
0
votes
1
reply
1.2k
views
single probe represent multiple genes?
gcrma
microarray
expressionset
updated 7.2 years ago by
svlachavas
▴ 830 • written 7.2 years ago by
mathavanbioinfo
▴ 20
4
votes
3
replies
1.2k
views
How to set custom Brainarray annotation for Biobase ExpressionSet object?
affymetrix microarrays
expressionset
biobase
annotation
brainarray
updated 6.8 years ago by
James W. MacDonald
65k • written 6.8 years ago by
lykhenko.olexandr
• 0
0
votes
1
reply
1.1k
views
Problem Subsetting ExpressionSet
expressionset
biobase
bioconductor
updated 6.9 years ago by
James W. MacDonald
65k • written 6.9 years ago by
Tom Oates
▴ 60
1
vote
1
reply
1.1k
views
Generating ExpressionSet Objects
r
expressionset
subseq
rnaseq
updated 7.8 years ago by
Martin Morgan
25k • written 7.8 years ago by
rrcutler
▴ 70
1
vote
1
reply
1.0k
views
Combining more than 2 ExpressionSets at the same time,
expressionset
combine
concatenate
combineTwoExpressionSet
8.0 years ago
g_draculla
▴ 10
0
votes
2
replies
985
views
'GO_analyse' function error
goexpress
ExpressionSet
GO_analyse
4.6 years ago
rezashiralmohammad
• 0
0
votes
0
replies
966
views
Error in building expression set for ArrayExpress
microarray
expressionset
arrayexpress
bioconductor
r
6.1 years ago
rf
• 0
0
votes
1
reply
961
views
ExpressionSet: Internal Standard
expressionset
updated 7.9 years ago by
Steve Lianoglou
★ 13k • written 7.9 years ago by
Herbert Meyer
• 0
0
votes
1
reply
920
views
beadarray error conversion
beadarray
limma
ExpressionSet
updated 7.4 years ago by
Gordon Smyth
50k • written 7.4 years ago by
emiliomastriani
• 0
0
votes
0
replies
852
views
HTqPCR - unable to create a 'qPCRset' object
htqpcr
expressionset
5.8 years ago
jirkanov
• 0
5
votes
2
replies
844
views
Is the ExpressionSet Class Deprecated?
expressionset
updated 3.6 years ago by
Martin Morgan
25k • written 3.6 years ago by
cannin
▴ 20
8
votes
23
replies
840
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 13 days ago by
Robert Castelo
★ 3.3k • written 14 days ago by
Bine
▴ 40
0
votes
0
replies
723
views
Computing se.exprs in R for an Expressionset?
microarray
Expressionset
se.exprs
5.7 years ago
payam_delfani1980
• 0
0
votes
1
reply
680
views
Calculations (averaging and normalization) with expressionset
RTCA
Biobase
Bioconductor
expressionset
updated 3.4 years ago by
James W. MacDonald
65k • written 3.4 years ago by
VanessaOak
• 0
0
votes
1
reply
499
views
ExpressionSet: any shortcut for number-of-samples and number-of-features?
expressionSet
4.0 years ago
aush
▴ 40
1
vote
2
replies
212
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
29 days ago
Mj.A.
• 0
36 results • Page
1 of 1
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Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: Adding a group of samples reduces DEGs in other groups
Answer: Gene set analysis: GSVA, Z-Score, and fold-changes
Answer: FilterByExpr low counts with small sample size
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
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