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rma
•
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0
votes
5
replies
1.6k
views
oligo rma() background normalization crash in basicRMA()
basicRMA
crash
rma
oligo
2.2 years ago
Steffen Moeller
▴ 90
1
vote
1
reply
1.2k
views
Strange error with RMA during Affymetrix data analysis
AffymetrixChip
RMA
updated 2.4 years ago by
Mike Smith
★ 6.6k • written 2.4 years ago by
Sara
▴ 20
4
votes
6
replies
1.7k
views
RMA on different disease labels
rma
background
microarray
normalization
updated 3.5 years ago by
James W. MacDonald
68k • written 3.5 years ago by
Joshua
• 0
1
vote
2
replies
1.5k
views
oligo package blas error
rma
openblas
blas
oligo
3.6 years ago
ch_el
▴ 10
0
votes
2
replies
1.4k
views
Ask for help on the preprocessing of GEO microarray data with Oligo and affy package
affy
rma
frma
oligo
updated 5.4 years ago by
James W. MacDonald
68k • written 5.4 years ago by
chziy429
• 0
1
vote
1
reply
717
views
RMA for multiple samples
biostatistic
RMA
updated 5.6 years ago by
James W. MacDonald
68k • written 5.6 years ago by
ijvechetti
▴ 10
0
votes
5
replies
2.6k
views
Install a custom CDF file
makecdf
RMA
annotation
biobase
GEOquery
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
Seymoo
• 0
0
votes
2
replies
1.3k
views
R: rma() function error
rma
normalization
microarray
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
get3232
• 0
1
vote
2
replies
1.8k
views
Inconsistent results when normalizing HTA2.0 arrays at "level=core"
oligo
HTA2.0
affycoretools
RMA
fitProbeLevelModel
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
Guido Hooiveld
★ 4.1k
2
votes
5
replies
1.5k
views
Error in get(cdfname, object 'mm430mmentrezgcdf' not found
affy
cdf
rma
updated 6.4 years ago by
Guido Hooiveld
★ 4.1k • written 6.4 years ago by
Walter Jessen
• 0
1
vote
0
replies
1.8k
views
Problems running oligo functions in parallel on a linux computer
biocparallel
oligo
rma
linux
parallel
7.3 years ago
s.munster
▴ 40
0
votes
5
replies
2.2k
views
Probe summerization of Human HT-12 V4 BeadChip arrays
beadarray
bead chip
illuminahumanv4.db
normalization
RMA
updated 7.4 years ago by
James W. MacDonald
68k • written 7.4 years ago by
Seymoo
• 0
0
votes
1
reply
1.6k
views
oligo rma() function giving unused argument error
oligo
rma
updated 8.0 years ago by
James W. MacDonald
68k • written 8.0 years ago by
Jiayi Sun
▴ 40
0
votes
3
replies
3.6k
views
how to use log2 transformation and limma
RMA
normalization
8.1 years ago
nia
▴ 30
2
votes
1
reply
1.8k
views
BrainArray Custom CDFs and oligo
oligo
brainarray
rma
customcdf
updated 8.2 years ago by
James W. MacDonald
68k • written 8.2 years ago by
lcordeiro
• 0
2
votes
1
reply
1.3k
views
perform probe level RMA without summarization
u133a
normalization
rma
affy
updated 8.3 years ago by
James W. MacDonald
68k • written 8.3 years ago by
jxd_84
▴ 10
0
votes
1
reply
1.1k
views
Microarray normalization---RMA and / or centering+scaling?
microarray
normalization
rma
updated 8.6 years ago by
James W. MacDonald
68k • written 8.6 years ago by
michaericalribo
• 0
3
votes
3
replies
3.1k
views
Problem using RMA Method in 'Oligo' with HTAFeatureset Objects
affymetrix microarrays
microarray
pd.hta.2.0
oligo
rma
updated 9.1 years ago by
James W. MacDonald
68k • written 9.1 years ago by
jennifer.drake
• 0
2
votes
3
replies
2.8k
views
RAW data in matrix: RMA normalization?
RMA
affy
raw expression
updated 9.3 years ago by
James W. MacDonald
68k • written 9.3 years ago by
alexvpickering
▴ 110
0
votes
1
reply
2.0k
views
PLIER normalization for Affymetrix GeneChip arrays?
microarray
affymetrix
oligo
RMA
normalization
updated 9.4 years ago by
James W. MacDonald
68k • written 9.4 years ago by
Nathaniel
▴ 20
0
votes
1
reply
1.9k
views
Error when running "eset <- rma(affyRaw)"
rma
updated 9.4 years ago by
Axel Klenk
★ 1.1k • written 9.4 years ago by
mochammad.ichsan87
• 0
0
votes
1
reply
1.2k
views
Looking for a package allowing Affymetrix MoGene2.1ST processing
affy
xps
rma
oligo
updated 9.4 years ago by
Guido Hooiveld
★ 4.1k • written 9.4 years ago by
steppydeklin
▴ 10
0
votes
2
replies
2.3k
views
Error with Normalization using (rma) method !!!
normalization
rma
updated 9.4 years ago by
James W. MacDonald
68k • written 9.4 years ago by
libya.tahani
• 0
2
votes
5
replies
6.1k
views
Oligo package RMA() function giving error
oligo
rma
updated 9.7 years ago by
Benilton Carvalho
★ 4.3k • written 9.7 years ago by
Jo
▴ 30
1
vote
7
replies
3.2k
views
reading a *.txt file of expression values into an AffyBatch
affy
normalization
rma
updated 9.8 years ago by
James W. MacDonald
68k • written 9.8 years ago by
m
• 0
1
vote
4
replies
1.8k
views
mutually add a tab in the beggining of the header to make it a valid RMA format
software error
probe
affy
RMA
9.8 years ago
Angel
▴ 40
0
votes
1
reply
1.9k
views
Reading in and normalising ht-hgu133a and hgu133a files together
hgu133a
rma
normalization
affy
updated 10.0 years ago by
svlachavas
▴ 840 • written 10.0 years ago by
parisa_1986
• 0
27 results • Page
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Comment: Differing results with DESeq2
by
JKim
• 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE
by
James W. MacDonald
68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation
by
sergisayolspuig
▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2
by
cold.wolverine.arku
• 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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