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hta2.0
•
reset
0
votes
2
replies
882
views
What is the best way to do annotation of the transcript clusters and filter in HTA 2.0
HTA2.0
microarray
affy
r
3.2 years ago
Marco_aurelio
• 0
2
votes
7
replies
1.1k
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy
rna
hta2.0
r
updated 3.5 years ago by
James W. MacDonald
64k • written 3.5 years ago by
Marco_aurelio
• 0
1
vote
2
replies
1.2k
views
Inconsistent results when normalizing HTA2.0 arrays at "level=core"
oligo
HTA2.0
affycoretools
RMA
fitProbeLevelModel
updated 4.4 years ago by
James W. MacDonald
64k • written 4.4 years ago by
Guido Hooiveld
★ 3.8k
4
votes
4
replies
985
views
arrayQualityMetrics in reading HTAfeatureSet read by oligo package
microarray
hta2.0
arrayqualitymetrics
updated 5.0 years ago by
Mike Smith
★ 6.2k • written 5.0 years ago by
RV
▴ 10
0
votes
5
replies
1.6k
views
Help for Affymetrix HTA 2.0 [transcript (gene) version] annotation
hta2.0
annotation
transcripts
updated 5.2 years ago by
svlachavas
▴ 820 • written 5.2 years ago by
Biomed
• 0
2
votes
8
replies
1.7k
views
Transcript-level SCAN.UPC preprocessing for Affymetrix HTA 2.0 arrays
microarray
scan.upc
hta2.0
updated 5.9 years ago by
Stephen Piccolo
▴ 590 • written 5.9 years ago by
Lukas__
• 0
1
vote
3
replies
1.2k
views
Use of RMA to get exon-level summaries for HTA 2.0
differential exon usage
exon array analysis
annotation
hta2.0
diffsplice
updated 6.2 years ago by
James W. MacDonald
64k • written 6.2 years ago by
relathman
▴ 20
2
votes
3
replies
1.3k
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 6.3 years ago by
James W. MacDonald
64k • written 6.3 years ago by
relathman
▴ 20
2
votes
7
replies
2.5k
views
HTA 2.0 and Transcript level analysis
hta2.0
transcripts
6.3 years ago
giroudpaul
▴ 40
0
votes
0
replies
973
views
segfault when trying to convert hta20_Hs_ENSE_22.cdf to binary format
affxparser
cdf
hta2.0
6.4 years ago
relathman
▴ 20
0
votes
0
replies
1.2k
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0
limma
batch effect
affymetrix microarrays
ComBat
6.6 years ago
svlachavas
▴ 820
2
votes
3
replies
1.5k
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 6.7 years ago by
James W. MacDonald
64k • written 6.7 years ago by
svlachavas
▴ 820
6
votes
7
replies
3.0k
views
Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with oligo for DE analysis
oligo
affycoretools
hta2.0
affymetrix
updated 18 months ago by
Yang Shi
▴ 10 • written 6.7 years ago by
svlachavas
▴ 820
0
votes
0
replies
799
views
(strange?) memory problem when running fitPLM on a set of HTA 2.0 arrays
affyPLM
fitPLM
hta2.0
7.2 years ago
Guido Hooiveld
★ 3.8k
14 results • Page
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Comment: Why is DMRcate not available for Bioconductor version 3.18?
by
Daniel E. Weeks
▴ 20
Thank you for the explanation and contacting the DSS package authors.
Comment: Why is DMRcate not available for Bioconductor version 3.18?
by
shepherl
3.6k
The DSS package authors just need to add `edgeR` to their Suggest of their DESCRIPTION. They have been contacted about it but have not acte…
Answer: GOslim missing GO term
by
James W. MacDonald
64k
I think it's because that GO term isn't an offspring of any term in the GO slim you are downloading. ``` > ids<- "GO:0002831" > slim <…
Answer: Obtaining rsIDs with ENSG and variant ID information
by
Robert Castelo
★ 3.0k
You should first and foremost find out what was the human reference genome version from which your dataset was derived. Assuming this was G…
Comment: DESeq2 - groups with biological replicates from the same patient
by
James W. MacDonald
64k
If by clustering you mean there might be a within-subject correlation, then yes it's a possibility. But you cannot control for that using a…
Votes
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: limma::voom vs edgeR::voomLmFit - when to use?
Answer: limma::voom vs edgeR::voomLmFit - when to use?
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