User: C T

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C T90
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90
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United States
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2 days, 19 hours ago
Joined:
6 years, 7 months ago
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Posts by C T

<prev • 36 results • page 1 of 4 • next >
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Comment: C: Error in creating BSGenome package
... upvoting just because of how nice you wrote the comment. Other people need to do this more often :-) ...
written 2 days ago by C T90
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Comment: C: emptyDrops identified less non-empty cells with lower total UMI counts?
... 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 7 weeks ago by C T90
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emptyDrops identified less non-empty cells with lower total UMI counts?
... 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 ...
simplesinglecell dropletutils scrna-seq cell calling emptydrops written 7 weeks ago by C T90 • updated 7 weeks ago by Aaron Lun25k
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Advice on correcting for batch effect using DESeq2
... 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 ...
deseq2 written 5 months ago by C T90 • updated 5 months ago by Michael Love25k
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Comment: C: Dispersion fit and p-value distributions
... 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 12 months ago by C T90
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Comment: C: Dispersion fit and p-value distributions
... 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 12 months ago by C T90
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Comment: C: Dispersion fit and p-value distributions
... 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 12 months ago by C T90
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Dispersion fit and p-value distributions
... 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 ...
rnaseq deseq2 fdrtool written 12 months ago by C T90 • updated 12 months ago by Ryan C. Thompson7.4k
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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 16 months ago by C T90
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Comment: C: DESeq2 PCA plot on fitted values
... *moved it down ...
written 16 months ago by C T90

Latest awards to C T

Popular Question 11 months ago, created a question with more than 1,000 views. For nearest genes using TxDb.Hsapiens.UCSC.hg19
Student 16 months ago, asked a question with at least 3 up-votes. For Dispersion fit and p-value distributions

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