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PCAtools
•
reset
5
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6
replies
245
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools
edgeR
pcaExplorer
RNASeq
RNAseq123
4 weeks ago
Alan
• 0
4
votes
8
replies
838
views
Interpreting ellipses in PCAtools for bulk RNAseq
ellipse
RNAseq
PCAtools
written 11 months ago by
elizabethe819
• 0
3
votes
2
replies
282
views
PCAtools lables missing or out of the plot
PCAtools
14 months ago
luca.s
▴ 10
3
votes
3
replies
527
views
PCAtools - change colour of points
PCAtools
updated 15 months ago by
Kevin Blighe
3.5k • written 15 months ago by
Terra
• 0
3
votes
15
replies
1.1k
views
How to ellipse a subset of data PCA biplot?
biplot
PCA
RNASeq
PCAtools
updated 17 months ago by
Kevin Blighe
3.5k • written 17 months ago by
mschmidt
▴ 10
0
votes
1
reply
509
views
Perform a biplot from pcaData and coldata in DESeq2, maybe PCAtools?
PCAtools
biplot
DESeq2
RNASeq
PCA
updated 18 months ago by
Kevin Blighe
3.5k • written 18 months ago by
ecg1g15
• 0
1
vote
3
replies
511
views
PCATools: is it possible to output a single legend when using pairsplot()?
PCATools
updated 19 months ago by
Kevin Blighe
3.5k • written 19 months ago by
oakhamwolf
• 0
2
votes
4
replies
623
views
Comparing discrete variable to PCA
EDA
pcaExplorer
PCAtools
PCA
updated 5 months ago by
Miguel
▴ 10 • written 21 months ago by
k.vitting.seerup
▴ 100
8 results • Page
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Comment: Quantile Normalization after rma or not?
by
Yang Shi
• 0
Got that sir! Really thank you!
Answer: Is it necessary to standardize Combat in R?
by
James W. MacDonald
59k
If you already have normalized data, then there is no reason to do something else like centering or scaling the data.
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
by
James W. MacDonald
59k
There are some QC probes that you might use. ``` > library(pd.hg.u219) > library(DBI) > con <- db(pd.hg.u219) > dbListTables(con) […
Comment: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
by
Bine
▴ 20
Thank you. The jpg it creates this way is empty. Remember I am doing it in R Notebook. But it did work with ggsave(). Many thanks
Comment: How to best visualize multi-level transcriptomics experiment data?
by
mohammedtoufiq91
▴ 10
@aliibarry Sure, let me try `rowVars`.
Votes
Comment: Quantile Normalization after rma or not?
Comment: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
Comment: How to best visualize multi-level transcriptomics experiment data?
Answer: How to best visualize multi-level transcriptomics experiment data?
A: redundant probe sets in Affymetrix HG-U219
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