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HTA2.0
•
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0
votes
2
replies
1.0k
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
1.8k
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 6.3 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 6.6 years ago by
James W. MacDonald
65k • written 6.6 years ago by
relathman
▴ 20
2
votes
3
replies
1.4k
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
6.8 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 7.0 years ago by
James W. MacDonald
65k • written 7.0 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 23 months ago by
Yang Shi
▴ 10 • written 7.0 years ago by
svlachavas
▴ 830
0
votes
0
replies
877
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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Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
Right, I was suggesting subsetting as a valid choice for "treatment and control samples at each timepoint"
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Fair enough, I guess it depends on the comparison being made, right? If one was interested in a feature comparing Timepoint A vs B, then it…
Comment: DESeq2 setting significant p-value
by
Dev
• 0
Sir but when I put in the expression data via the csv file, it was showing the gene names then but now when i set it in the form factor it …
Answer: OrgDb for maize
by
James W. MacDonald
65k
``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% snapshotDate(): 2023-10-23 > query(hu…
Comment: Which input file is used for DGEList in EgdeR?
by
i.atanasoai
• 0
Understood, Thank you very much for the reply, very kind.
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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