User: Kristina M Fontanez

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Posts by Kristina M Fontanez

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Error installing development version of DESeq2
... Mike- I tried downloading the development version of DESeq2 following your directions but it didn’t work. It seems I have 2 problems, 1) I am not using the development version of R (3.1) and therefore this prevents me from using the development version of Bioconductor (2.14). Is that right? I don’t ...
gui deseq2 written 5.6 years ago by Kristina M Fontanez220 • updated 5.6 years ago by Dan Tenenbaum8.2k
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Comment: C: DEseq2 metagenomic analysis without replicates
... Hi Mike- Is there any reason NOT to convert the log2 counts back into expected counts using 2^(expected count after shrinking)? I want to avoid the negative values and by converting the data back into expected counts I can easily create relative abundance plots by calculating expected count for fe ...
written 5.6 years ago by Kristina M Fontanez220
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Comment: C: DESeq2: NA on padj column when doing bonferroni
... David- I’m sorry but I didn’t really understand your question. I don’t know what you mean by Carboniferous, raw value (p-value?) or pad (p-adjusted value?). However, this section (pg 8) of the vignette may help you determine why you have NAs in the p-value column or the p-adjusted column in your r ...
written 5.6 years ago by Kristina M Fontanez220
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Comment: C: DESeq2: NA on padj column when doing bonferroni
... Hi David, Hi Kristina, That was it indeed, thanks a lot. But then again, why do I not get them, the NAs I mean, when I do BH on the same data and the same contrast? That is: results(dds,resultsNames(dds)[i],pAdjustMethod="BH") Thanks again, Best, David One likely possibility: Independent Filter ...
written 5.6 years ago by Kristina M Fontanez220
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Answer: A: DESeq2: NA on padj column when doing bonferroni
... Hi David- If you look at the description of results() in the manual then you will see that by default independentFiltering is turned ON. I think this is your likely culprit given that your results function call doesn’t explicitly turn OFF independent filtering. pg.27: "By default, independent filt ...
written 5.6 years ago by Kristina M Fontanez220
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Comment: C: DEseq2 metagenomic analysis without replicates
... Hi Mike- Thanks for the clarification below - I don’t know how I missed that. ​No, it does account for sequencing. We say explicitly in the vignette and man pages that the rlog is better for accounting for size factors differences than VST. Also the formulae provided in the vignette and man p ...
written 5.6 years ago by Kristina M Fontanez220
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Comment: C: DEseq2 metagenomic analysis without replicates
... Mike and Simon, Thank you for your detailed answers to my questions. I’ve learned a great deal from this discussion thus far. Below I have summarized and added a few additional questions. In order to present relative abundance barcharts/heatmaps I should use regularized log transformed data, whi ...
written 5.6 years ago by Kristina M Fontanez220
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Answer: A: DEseq2 metagenomic analysis without replicates
... **I am including an earlier message which I neglected to cc to the Bioconductor forum, pasted below** Mike- Just one more short, related question - why is it that some of the rlogTransformed counts have negative values? I can certainly just add 1 to all of the values in order to make plotting rela ...
written 5.6 years ago by Kristina M Fontanez220
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Comment: C: DEseq2 metagenomic analysis without replicates
... Hi Simon- Thank you for your detailed reply. I agree that it is the case often in marine microbiology that the null hypothesis of no changes between treatments, often does not really apply. When you frame the discussion this way, it makes sense that I am seeing large numbers of differentially abund ...
written 5.6 years ago by Kristina M Fontanez220
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Comment: C: DEseq2 metagenomic analysis without replicates
... Simon- Thank you again for your help answering all of my questions. I really appreciate the time you?ve taken on this problem. For the dead vs seawater comparison, 111/ 344 with p-adjusted values <1e-5 have log2Fold changes of > 3 or < -3. So, if I use that as my significance threshold - ...
written 5.6 years ago by Kristina M Fontanez220

Latest awards to Kristina M Fontanez

Great Question 5.6 years ago, created a question with more than 5,000 views. For DESeq2 pitfalls of rlog transformation
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Error installing development version of DESeq2
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Error installing development version of DESeq2

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