User: C T

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C T90
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5 years, 7 months ago
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Posts by C T

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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 24 days 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 24 days 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 24 days 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 25 days ago by C T90 • updated 24 days ago by Ryan C. Thompson7.0k
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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 4 months ago by C T90
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Comment: C: DESeq2 PCA plot on fitted values
... *moved it down ...
written 4 months ago by C T90
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Comment: 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 14 months ago by C T90
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Comment: 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 14 months ago by C T90
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reads alignment statistics
... 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, ...
rsubread bioconductor written 14 months ago by C T90 • updated 13 months ago by Hervé Pagès ♦♦ 13k
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PCR bottleneck coefficient (PBC)
... 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? ...
chipqc written 16 months ago by C T90 • updated 16 months ago by Rory Stark2.6k

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Student 4 months ago, asked a question with at least 3 up-votes. For Dispersion fit and p-value distributions

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