User: C T

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C T • 90
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90
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United States
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6 years, 3 months ago
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Posts by C T

<prev • 33 results • page 1 of 4 • next >
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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 10 weeks ago by C T • 90 • updated 10 weeks ago by Michael Love ♦ 24k
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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 9 months ago by C T • 90
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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 9 months ago by C T • 90
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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 9 months ago by C T • 90
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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 9 months ago by C T • 90 • updated 9 months ago by Ryan C. Thompson ♦ 7.3k
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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 13 months ago by C T • 90
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Comment: C: DESeq2 PCA plot on fitted values
... *moved it down ...
written 13 months ago by C T • 90
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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 22 months ago by C T • 90
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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 22 months ago by C T • 90
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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 22 months ago by C T • 90 • updated 22 months ago by Hervé Pagès ♦♦ 14k

Latest awards to C T

Popular Question 8 months ago, created a question with more than 1,000 views. For nearest genes using TxDb.Hsapiens.UCSC.hg19
Student 13 months ago, asked a question with at least 3 up-votes. For Dispersion fit and p-value distributions
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