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hta2.0
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0
votes
2
replies
1.1k
views
What is the best way to do annotation of the transcript clusters and filter in HTA 2.0
HTA2.0
microarray
affy
r
3.6 years ago
Marco_aurelio
• 0
2
votes
7
replies
1.2k
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy
rna
hta2.0
r
updated 3.9 years ago by
James W. MacDonald
65k • written 3.9 years ago by
Marco_aurelio
• 0
1
vote
2
replies
1.4k
views
Inconsistent results when normalizing HTA2.0 arrays at "level=core"
oligo
HTA2.0
affycoretools
RMA
fitProbeLevelModel
updated 4.8 years ago by
James W. MacDonald
65k • written 4.8 years ago by
Guido Hooiveld
★ 3.9k
4
votes
4
replies
1.1k
views
arrayQualityMetrics in reading HTAfeatureSet read by oligo package
microarray
hta2.0
arrayqualitymetrics
updated 5.4 years ago by
Mike Smith
★ 6.5k • written 5.4 years ago by
RV
▴ 10
0
votes
5
replies
1.9k
views
Help for Affymetrix HTA 2.0 [transcript (gene) version] annotation
hta2.0
annotation
transcripts
updated 5.6 years ago by
svlachavas
▴ 830 • written 5.6 years ago by
Biomed
• 0
2
votes
8
replies
1.9k
views
Transcript-level SCAN.UPC preprocessing for Affymetrix HTA 2.0 arrays
microarray
scan.upc
hta2.0
updated 6.3 years ago by
Stephen Piccolo
▴ 590 • written 6.4 years ago by
Lukas__
• 0
1
vote
3
replies
1.4k
views
Use of RMA to get exon-level summaries for HTA 2.0
differential exon usage
exon array analysis
annotation
hta2.0
diffsplice
updated 6.7 years ago by
James W. MacDonald
65k • written 6.7 years ago by
relathman
▴ 20
2
votes
3
replies
1.5k
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 6.7 years ago by
James W. MacDonald
65k • written 6.7 years ago by
relathman
▴ 20
2
votes
7
replies
2.7k
views
HTA 2.0 and Transcript level analysis
hta2.0
transcripts
6.7 years ago
giroudpaul
▴ 40
0
votes
0
replies
1.1k
views
segfault when trying to convert hta20_Hs_ENSE_22.cdf to binary format
affxparser
cdf
hta2.0
6.9 years ago
relathman
▴ 20
0
votes
0
replies
1.3k
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0
limma
batch effect
affymetrix microarrays
ComBat
7.0 years ago
svlachavas
▴ 830
2
votes
3
replies
1.6k
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 7.1 years ago by
James W. MacDonald
65k • written 7.1 years ago by
svlachavas
▴ 830
6
votes
7
replies
3.2k
views
Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with oligo for DE analysis
oligo
affycoretools
hta2.0
affymetrix
updated 24 months ago by
Yang Shi
▴ 10 • written 7.1 years ago by
svlachavas
▴ 830
0
votes
0
replies
895
views
(strange?) memory problem when running fitPLM on a set of HTA 2.0 arrays
affyPLM
fitPLM
hta2.0
7.6 years ago
Guido Hooiveld
★ 3.9k
14 results • Page
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Answer: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Comment: DNAString: Standard checksum function?
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Henrik Bengtsson
★ 2.4k
For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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