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RMA
•
reset
0
votes
5
replies
1.9k
views
oligo rma() background normalization crash in basicRMA()
basicRMA
crash
rma
oligo
2.7 years ago • updated 2.6 years ago
Steffen Moeller
▴ 90
1
vote
1
reply
1.3k
views
Strange error with RMA during Affymetrix data analysis
AffymetrixChip
RMA
updated 2.9 years ago by
Mike Smith
★ 6.6k • written 2.9 years ago by
Sara
▴ 20
4
votes
6
replies
1.9k
views
RMA on different disease labels
rma
background
microarray
normalization
updated 4.0 years ago by
James W. MacDonald
68k • written 4.0 years ago by
Joshua
• 0
1
vote
2
replies
1.7k
views
oligo package blas error
rma
openblas
blas
oligo
4.1 years ago
ch_el
▴ 10
0
votes
2
replies
1.6k
views
Ask for help on the preprocessing of GEO microarray data with Oligo and affy package
affy
rma
frma
oligo
updated 5.9 years ago by
James W. MacDonald
68k • written 5.9 years ago by
chziy429
• 0
1
vote
1
reply
795
views
RMA for multiple samples
biostatistic
RMA
updated 6.1 years ago by
James W. MacDonald
68k • written 6.1 years ago by
ijvechetti
▴ 10
0
votes
5
replies
2.9k
views
Install a custom CDF file
makecdf
RMA
annotation
biobase
GEOquery
updated 6.3 years ago by
James W. MacDonald
68k • written 6.3 years ago by
Seymoo
• 0
0
votes
2
replies
1.4k
views
R: rma() function error
rma
normalization
microarray
updated 6.3 years ago by
James W. MacDonald
68k • written 6.3 years ago by
get3232
• 0
1
vote
2
replies
1.9k
views
Inconsistent results when normalizing HTA2.0 arrays at "level=core"
oligo
HTA2.0
affycoretools
RMA
fitProbeLevelModel
updated 6.3 years ago by
James W. MacDonald
68k • written 6.3 years ago by
Guido Hooiveld
★ 4.1k
2
votes
5
replies
1.6k
views
Error in get(cdfname, object 'mm430mmentrezgcdf' not found
affy
cdf
rma
updated 6.9 years ago by
Guido Hooiveld
★ 4.1k • written 6.9 years ago by
Walter Jessen
• 0
1
vote
0
replies
1.9k
views
Problems running oligo functions in parallel on a linux computer
biocparallel
oligo
rma
linux
parallel
7.8 years ago
s.munster
▴ 40
0
votes
5
replies
2.5k
views
Probe summerization of Human HT-12 V4 BeadChip arrays
beadarray
bead chip
illuminahumanv4.db
normalization
RMA
updated 7.9 years ago by
James W. MacDonald
68k • written 7.9 years ago by
Seymoo
• 0
0
votes
1
reply
1.6k
views
oligo rma() function giving unused argument error
oligo
rma
updated 8.5 years ago by
James W. MacDonald
68k • written 8.5 years ago by
Jiayi Sun
▴ 40
0
votes
3
replies
3.7k
views
how to use log2 transformation and limma
RMA
normalization
8.6 years ago
nia
▴ 30
2
votes
1
reply
2.0k
views
BrainArray Custom CDFs and oligo
oligo
brainarray
rma
customcdf
updated 8.7 years ago by
James W. MacDonald
68k • written 8.7 years ago by
lcordeiro
• 0
2
votes
1
reply
1.4k
views
perform probe level RMA without summarization
u133a
normalization
rma
affy
updated 8.8 years ago by
James W. MacDonald
68k • written 8.8 years ago by
jxd_84
▴ 10
0
votes
1
reply
1.1k
views
Microarray normalization---RMA and / or centering+scaling?
microarray
normalization
rma
updated 9.1 years ago by
James W. MacDonald
68k • written 9.1 years ago by
michaericalribo
• 0
3
votes
3
replies
3.2k
views
Problem using RMA Method in 'Oligo' with HTAFeatureset Objects
affymetrix microarrays
microarray
pd.hta.2.0
oligo
rma
updated 9.6 years ago by
James W. MacDonald
68k • written 9.6 years ago by
jennifer.drake
• 0
2
votes
3
replies
2.9k
views
RAW data in matrix: RMA normalization?
RMA
affy
raw expression
updated 9.8 years ago by
James W. MacDonald
68k • written 9.8 years ago by
alexvpickering
▴ 110
0
votes
1
reply
2.1k
views
PLIER normalization for Affymetrix GeneChip arrays?
microarray
affymetrix
oligo
RMA
normalization
updated 9.9 years ago by
James W. MacDonald
68k • written 9.9 years ago by
Nathaniel
▴ 20
0
votes
1
reply
2.0k
views
Error when running "eset <- rma(affyRaw)"
rma
updated 9.9 years ago by
Axel Klenk
★ 1.1k • written 9.9 years ago by
mochammad.ichsan87
• 0
0
votes
1
reply
1.3k
views
Looking for a package allowing Affymetrix MoGene2.1ST processing
affy
xps
rma
oligo
updated 9.9 years ago by
Guido Hooiveld
★ 4.1k • written 9.9 years ago by
steppydeklin
▴ 10
0
votes
2
replies
2.4k
views
Error with Normalization using (rma) method !!!
normalization
rma
updated 9.9 years ago by
James W. MacDonald
68k • written 9.9 years ago by
libya.tahani
• 0
2
votes
5
replies
6.3k
views
Oligo package RMA() function giving error
oligo
rma
updated 10.2 years ago by
Benilton Carvalho
★ 4.3k • written 10.2 years ago by
Jo
▴ 30
1
vote
7
replies
3.5k
views
reading a *.txt file of expression values into an AffyBatch
affy
normalization
rma
updated 10.3 years ago by
James W. MacDonald
68k • written 10.3 years ago by
m
• 0
1
vote
4
replies
1.9k
views
mutually add a tab in the beggining of the header to make it a valid RMA format
software error
probe
affy
RMA
10.3 years ago
Angel
▴ 40
0
votes
1
reply
2.0k
views
Reading in and normalising ht-hgu133a and hgu133a files together
hgu133a
rma
normalization
affy
updated 10.5 years ago by
svlachavas
▴ 840 • written 10.5 years ago by
parisa_1986
• 0
27 results • Page
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Replies
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
Was anyone else able to put the pieces together using the reply above? I read in one 10X sample using DropletUtils::read10xCounts() and thi…
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G
by
dzv20413
• 0
Wow, GBCC 2025 sounds amazing, can not wait to see the logo contest results! Also, I just played [Level Devil][1] and it is super addictive…
Comment: Memory error while running alignments
by
Erik Wright
▴ 150
How much memory is available on the computer? A distance matrix of 50k sequences requires at least 50k*50k/2 * 8 bytes = 10GB, assuming the…
Votes
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
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