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clariom
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Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom
Align
MicroarrayData
Alignment
Microarray
13 months ago
jsharif
• 0
1
vote
5
replies
1.2k
views
Correct annotation R package for human clariom array analysis
clariom
oligo
affycoretools
pd.hugene.2.0.st
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
svlachavas
▴ 830
1
vote
3
replies
842
views
Selecting probe data from Clariom D assays using the fid probe tags
clariom
pd.clariom.d.human
updated 5.5 years ago by
James W. MacDonald
65k • written 5.5 years ago by
AliStair Rust
• 0
1
vote
1
reply
969
views
RNA degradation plot for Clariom S and Clariom D
Rna degradation
Clariom
updated 6.1 years ago by
James W. MacDonald
65k • written 6.1 years ago by
kritikamish99
▴ 10
2
votes
4
replies
2.2k
views
affycoretools annotateEset problem using Clariom D arrays
affycoretools
clariom
updated 6.6 years ago by
James W. MacDonald
65k • written 6.6 years ago by
willj
▴ 30
2
votes
2
replies
1.0k
views
paCalls with Clariom Chips
oligo
microarray
clariom
updated 6.7 years ago by
James W. MacDonald
65k • written 6.7 years ago by
kmvaldez2
• 0
0
votes
0
replies
774
views
genefu and clariom d
clariom
genefu
6.8 years ago
info
• 0
7 results • Page
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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.
Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
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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