## User: C T

C T •

**90**- Reputation:
**90**- Status:
- Trusted
- Location:
- United States
- Last seen:
- 2 months, 3 weeks ago
- Joined:
- 5 years, 10 months ago
- Email:
- t*******@osu.edu

#### Posts by C T

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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 3 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 3 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 3 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 3 months ago by
C T •

**90**• updated 3 months ago by Ryan C. Thompson ♦**7.1k**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 7 months ago by
C T •

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Comment:
C: DESeq2 PCA plot on fitted values

... *moved it down
...

written 7 months ago by
C T •

**90**1

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C: reads alignment statistics

... Thanks for your help. I figured it out.
I ran bowtie retaining only unique mapped reads. Therefore, my bam file does not contain multiple mapped reads. Duh!
James, thanks again for your help.
...

written 16 months ago by
C T •

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C: reads alignment statistics

... Thanks for the hints on countBam. However, I still cannot get the number of uniquely mapped reads.
I thought the following should return number of multiple mapped reads. However, it returns 0 when I know there are multiple mapped reads. bowtie2 shows ~14 millions reads
file='input.bam'
countBam(f ...

written 16 months ago by
C T •

**90**6

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... Hello...
Is there an R package that can calculate alignment statistics from bam/sam files? By alignment statistics I mean number of reads, number of reads uniquely mapped, number of reads mapped to multiple locations.
I found rsubread package can count number of reads that can be mapped. However, ...

written 16 months ago by
C T •

**90**• updated 16 months ago by Hervé Pagès ♦♦**13k**0

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... Is there a way to calculate the PBC1 and PBC2 following ENCODE standard https://www.encodeproject.org/data-standards/terms/#library?
I thought ChIPQC calculate these but I cannot find it?
...

written 18 months ago by
C T •

**90**• updated 18 months ago by Rory Stark •**2.7k**#### Latest awards to C T

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

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