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hta2.0
•
reset
0
votes
2
replies
410
views
Seeking Advice on HTA 2.0 Microarray Data Processing with Oligo Package
hta20transcriptcluster.db
org.Sc.sgd.db
HTA2.0
MicroRNAArrayData
10 weeks ago
Yao Lipu
• 0
0
votes
2
replies
1.4k
views
What is the best way to do annotation of the transcript clusters and filter in HTA 2.0
HTA2.0
microarray
affy
r
4.7 years ago • updated 4.6 years ago
Marco_aurelio
• 0
2
votes
7
replies
1.7k
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy
rna
hta2.0
r
updated 5.0 years ago by
James W. MacDonald
68k • written 5.0 years ago by
Marco_aurelio
• 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 5.9 years ago by
James W. MacDonald
68k • written 5.9 years ago by
Guido Hooiveld
★ 4.1k
4
votes
4
replies
1.5k
views
arrayQualityMetrics in reading HTAfeatureSet read by oligo package
microarray
hta2.0
arrayqualitymetrics
updated 6.4 years ago by
Mike Smith
★ 6.6k • written 6.4 years ago by
RV
▴ 10
0
votes
5
replies
2.6k
views
Help for Affymetrix HTA 2.0 [transcript (gene) version] annotation
hta2.0
annotation
transcripts
updated 6.7 years ago by
svlachavas
▴ 840 • written 6.7 years ago by
Biomed
• 0
2
votes
8
replies
2.4k
views
Transcript-level SCAN.UPC preprocessing for Affymetrix HTA 2.0 arrays
microarray
scan.upc
hta2.0
updated 7.4 years ago by
Stephen Piccolo
▴ 600 • written 7.4 years ago by
Lukas__
• 0
1
vote
3
replies
1.7k
views
Use of RMA to get exon-level summaries for HTA 2.0
differential exon usage
exon array analysis
annotation
hta2.0
diffsplice
updated 7.7 years ago by
James W. MacDonald
68k • written 7.7 years ago by
relathman
▴ 20
2
votes
3
replies
1.8k
views
Filtering of lowly expressed probes in HTA 2.0 using new pd.hta.2.0 version 3.12.2
pd.hta.2.0
hta2.0
affycoretools
updated 7.7 years ago by
James W. MacDonald
68k • written 7.7 years ago by
relathman
▴ 20
2
votes
7
replies
3.4k
views
HTA 2.0 and Transcript level analysis
hta2.0
transcripts
7.7 years ago
giroudpaul
▴ 40
0
votes
0
replies
1.3k
views
segfault when trying to convert hta20_Hs_ENSE_22.cdf to binary format
affxparser
cdf
hta2.0
7.9 years ago
relathman
▴ 20
0
votes
0
replies
1.5k
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0
limma
batch effect
affymetrix microarrays
ComBat
8.0 years ago
svlachavas
▴ 840
2
votes
3
replies
1.9k
views
Problem with memory limit in Rstudio/Windows when importing Affymetrix HTA 2.0 CEL files with oligo R package
oligo
hta2.0
affymetrix microarrays
memory problem
updated 8.1 years ago by
James W. MacDonald
68k • written 8.1 years ago by
svlachavas
▴ 840
6
votes
7
replies
3.8k
views
Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with oligo for DE analysis
oligo
affycoretools
hta2.0
affymetrix
updated 3.0 years ago by
Yang Shi
▴ 10 • written 8.1 years ago by
svlachavas
▴ 840
0
votes
0
replies
1.1k
views
(strange?) memory problem when running fitPLM on a set of HTA 2.0 arrays
affyPLM
fitPLM
hta2.0
8.7 years ago
Guido Hooiveld
★ 4.1k
15 results • Page
1 of 1
Recent ...
Replies
Comment: DiffBind - question on the use of filtered or unfiltered input data
by
sloperun3az
• 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash
by
sloperun3az
• 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr
by
Paul Harrison
▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use?
by
Gordon Smyth
52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Comment: limma::voom vs edgeR::voomLmFit - when to use?
by
Geoff
• 0
Just wondering--why was this function put into `edgeR` rather than `limma`? Maybe a bit technical, but it is a little confusing from an out…
Votes
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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