Moderator: Ryan C. Thompson

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Posts by Ryan C. Thompson

<prev • 731 results • page 1 of 74 • next >
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Comment: C: Normalize for changes in one direction
... I would say the first thing to do is to make an MA plot of your data. If it shows a bimodal distribution along the vertical (logFC) axis, then you might have some issues with the normalization, especially if neither mode is centered on zero. ...
written 5 days ago by Ryan C. Thompson6.3k
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Answer: A: Minimum in Voomplot
... No, I wouldn't say this is cause for concern. The upward trend at the high end is driven by the relatively few genes with such high abundances. It's not uncommon to see high-expression genes having high variability as well. ...
written 9 days ago by Ryan C. Thompson6.3k
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Comment: C: Removing batch effects from microarray data based on only a subset of samples
... The asker is already aware of this batch effect. It is captured in the batch variable of the sample table given in the original question. ...
written 25 days ago by Ryan C. Thompson6.3k
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Comment: C: Removing batch effects from microarray data based on only a subset of samples
... This is the first time you've mentioned the "line" variable. If this is what you were asking about, you should have mentioned it in the original question. Are you saying that you expect "CON LINE1 r1" and "CON LINE1 r2" to cluster with each other more tightly than they do with other controls? If so, ...
written 25 days ago by Ryan C. Thompson6.3k
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Answer: A: Applying SVA to RNA-Seq dataset
... It looks to me like SVA is helping quite a bit for this data set. I always like to plot the surrogate variables against any known confounding factors (such as RNA extraction date, in your case). If you can show that SVA is capturing the variation due to known confounders, that gives you confidence t ...
written 4 weeks ago by Ryan C. Thompson6.3k
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Comment: C: Help running the nondetects::qpcrImpute on my data?
... Ok, so I should simply replace my NA values with 40 (the maximum value), and then run the imputation algorithm? Edit: Doing so seems to have worked. ...
written 4 weeks ago by Ryan C. Thompson6.3k
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Answer: A: Normalized counts after fitting linear model with batch effects - edgeR
... Getting a matrix of batch-corrected counts is not really possible, because the resulting matrix would not represent actual counts. However, getting a matrix of batch-corrected logCPM values is certainly possible, using removeBatchEffect. Note that this kind of batch subtraction will likely change th ...
written 4 weeks ago by Ryan C. Thompson6.3k
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Comment: C: Normalized counts after fitting linear model with batch effects - edgeR
... This is not an answer to your question, but your design is almost completely confounded, since the second batch only has a single control sample. This means that the entire batch correction hinges on that single sample, and any noise in that sample will be interpreted as a batch effect to be subtrac ...
written 4 weeks ago by Ryan C. Thompson6.3k
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Comment: C: Help running the nondetects::qpcrImpute on my data?
... In case it matters, the design formula for this experiment is ~condition + animal. ...
written 5 weeks ago by Ryan C. Thompson6.3k
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Comment: C: Help running the nondetects::qpcrImpute on my data?
... Are you loading the file with readRDS? ...
written 5 weeks ago by Ryan C. Thompson6.3k

Latest awards to Ryan C. Thompson

Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Popular Question 9 months ago, created a question with more than 1,000 views. For Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?
Scholar 9 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 11 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 12 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Scholar 12 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Scholar 12 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 22 months ago, created an answer that has been accepted. For A: On the relationship between design and contrasts
Scholar 22 months ago, created an answer that has been accepted. For A: normalized data by DESeq2 look suspicious
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: DESeq2 how to define my conditions when I want the results comparing a subset of
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Usability of ERCC spike-ins in standard RNAseq experiments
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Accounting for 5'/3' Bias in DESeq 2
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: FDR and padj in deseq and edger
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: edger, trended or common dispersion
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Ribosome profiling analysis in DEseq2/limma
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: DE for genes with very low counts using limma.
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Using multiple tools for differential gene expression analysis as validation
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: edgeR RNA-seq analysis using glm

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