## User: C T

C T •

**90**- Reputation:
**90**- Status:
- Trusted
- Location:
- United States
- Last seen:
- 1 month, 2 weeks ago
- Joined:
- 6 years, 8 months ago
- Email:
- t*******@osu.edu

#### Posts by C T

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... upvoting just because of how nice you wrote the comment. Other people need to do this more often :-) ...

written 6 weeks ago by
C T •

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... Hi Aaron,
Thank you very much for your clear explanation. I have one more related question: in your f1000research paper, it didn't have cell calling step. It makes me wonder whether there are specific cases where you don't need to do cell calling. Thank you! ...

written 3 months ago by
C T •

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... Hello,
I hope someone can help me understand this better. I am running the emptyDrops method from DropletUtils library which distinguishes empty from non-empty cells. The function accepts lower parameter which specify the lower bound on the total UMI count, at or below which all barcodes are assume ...

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... Hello,
I am analyzing RNA-seq data using DESeq2
I have 5 groups of samples each with 4 replicates.
Below is a PCA plot of the VST transformed value:
![enter image description here][1]
as shown in the PCA plot, replicate 1 (R1) are separate from the others on the upper half of the PCA plot. There a ...

written 7 months ago by
C T •

**90**• updated 7 months ago by Michael Love ♦**26k**0

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... Thank you, Ryan! Your answer gives me things to consider and look for the next time I have the same problem with the p-value distribution. It's nice to know limma has function that can put less weight on outlier samples.
Thank you, Michael!
...

written 13 months ago by
C T •

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... Thank you for the insights on SVA.
This is the code that I ran to estimate the number of surrogate variables.
DESeq2Table <- estimateSizeFactors(dds)
dat <- counts(DESeq2Table, normalized = TRUE)
idx <- rowMeans(dat) > 1
dat <- dat[idx, ]
mod <- model.matrix(~ group, colData ...

written 13 months ago by
C T •

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... Hi Bernd,
Thank you so much for your advice. Really appreciate the time you took to read through my post and thank you for your kind words.
I am tempted to use the SVA + fdrtool result just because it gave me more genes to look at and also since you mentioned this approach is not wrong. However, I ...

written 13 months ago by
C T •

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... Hello,
I need advice on the RNA-seq analysis results that I did using DESeq2. I have 4 experiments each with 3 biological replicates. At first I analyzed them all together. I put in the batch effect in the DESeq2 model.
PCA plot of all the experiments together:
and the raw p-values distribution ...

written 13 months ago by
C T •

**90**• updated 13 months ago by Ryan C. Thompson ♦**7.4k**0

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Comment:
C: DESeq2 PCA plot on fitted values

... Sorry to revive this old thread. But, I just want to make sure.
So, if I do
plotMDS(log(t( t(assays(dds)[["mu"]]) / sizeFactors(dds) ) + 1)
I am using the fitted values that include the batch effect, correct? So, if samples are closer together in this MDS plot, it should represents how similar t ...

written 17 months ago by
C T •

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Comment:
C: DESeq2 PCA plot on fitted values

... *moved it down
...

written 17 months ago by
C T •

**90**#### Latest awards to C T

Popular Question
13 months ago,
created a question with more than 1,000 views.
For nearest genes using TxDb.Hsapiens.UCSC.hg19

Student
17 months ago,
asked a question with at least 3 up-votes.
For Dispersion fit and p-value distributions

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