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hta2.0
•
reset
0
votes
2
replies
654
views
Seeking Advice on HTA 2.0 Microarray Data Processing with Oligo Package
hta20transcriptcluster.db
org.Sc.sgd.db
HTA2.0
MicroRNAArrayData
12 months ago
Yao Lipu
• 0
0
votes
2
replies
1.8k
views
What is the best way to do annotation of the transcript clusters and filter in HTA 2.0
HTA2.0
microarray
affy
r
5.5 years ago • updated 5.4 years ago
Marco_aurelio
• 0
2
votes
7
replies
2.0k
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy
rna
hta2.0
r
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
Marco_aurelio
• 0
1
vote
2
replies
2.0k
views
Inconsistent results when normalizing HTA2.0 arrays at "level=core"
oligo
HTA2.0
affycoretools
RMA
fitProbeLevelModel
updated 6.7 years ago by
James W. MacDonald
68k • written 6.7 years ago by
Guido Hooiveld
★ 4.1k
4
votes
4
replies
1.7k
views
arrayQualityMetrics in reading HTAfeatureSet read by oligo package
microarray
hta2.0
arrayqualitymetrics
updated 7.2 years ago by
Mike Smith
★ 6.6k • written 7.2 years ago by
RV
▴ 10
0
votes
5
replies
3.1k
views
Help for Affymetrix HTA 2.0 [transcript (gene) version] annotation
hta2.0
annotation
transcripts
updated 7.5 years ago by
svlachavas
▴ 840 • written 7.5 years ago by
Biomed
• 0
2
votes
8
replies
2.8k
views
Transcript-level SCAN.UPC preprocessing for Affymetrix HTA 2.0 arrays
microarray
scan.upc
hta2.0
updated 8.2 years ago by
Stephen Piccolo
▴ 600 • written 8.2 years ago by
Lukas__
• 0
1
vote
3
replies
2.0k
views
Use of RMA to get exon-level summaries for HTA 2.0
differential exon usage
exon array analysis
annotation
hta2.0
diffsplice
updated 8.5 years ago by
James W. MacDonald
68k • written 8.5 years ago by
relathman
▴ 20
2
votes
3
replies
2.0k
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 8.5 years ago by
James W. MacDonald
68k • written 8.5 years ago by
relathman
▴ 20
2
votes
7
replies
3.9k
views
HTA 2.0 and Transcript level analysis
hta2.0
transcripts
8.5 years ago
giroudpaul
▴ 40
0
votes
0
replies
1.5k
views
segfault when trying to convert hta20_Hs_ENSE_22.cdf to binary format
affxparser
cdf
hta2.0
8.7 years ago
relathman
▴ 20
0
votes
0
replies
1.7k
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0
limma
batch effect
affymetrix microarrays
ComBat
8.8 years ago
svlachavas
▴ 840
2
votes
3
replies
2.1k
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 8.9 years ago by
James W. MacDonald
68k • written 8.9 years ago by
svlachavas
▴ 840
6
votes
7
replies
4.4k
views
Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with oligo for DE analysis
oligo
affycoretools
hta2.0
affymetrix
updated 3.8 years ago by
Yang Shi
▴ 10 • written 8.9 years ago by
svlachavas
▴ 840
0
votes
0
replies
1.3k
views
(strange?) memory problem when running fitPLM on a set of HTA 2.0 arrays
affyPLM
fitPLM
hta2.0
9.5 years ago
Guido Hooiveld
★ 4.1k
15 results • Page
1 of 1
Recent ...
Replies
Comment: GSEA error
by
Adithi
• 0
Thank you so much. That makes perfect sense to me. I will work on this.
Comment: tximeta cannot open annotation gtf?
by
Michael Love
43k
Yes, so this is the same type of error you would get if you tried to assemble a *SummarizedExperiment* manually with tximport + GTF process…
Answer: tximeta cannot open annotation gtf?
by
ATpoint
★ 5.0k
> Timeout of 60 seconds was reached You have to increase the default timeout limits for downloads, `options(timeout=3600)`. GENCODE serve…
Answer: GSEA error
by
James W. MacDonald
68k
At a very high level, the way non-model organisms are annotated is by using blast to find orthologs in other species that are well annotate…
Comment: Unable to find ENTREZ IDs
by
Adithi
• 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Votes
Answer: GSEA error
Answer: OrgDb for maize
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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