User: Kristina M Fontanez

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Posts by Kristina M Fontanez

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Comment: C: DESeq2 pitfalls of rlog transformation
... Mike- Thank you for your suggestion to try the regularized log transformation with blind=FALSE. The variance in the blind=FALSE data appears more similar to the untransformed variance. sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9 sample10 sample11 ...
written 5.9 years ago by Kristina M Fontanez220
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Answer: A: DESeq2 pitfalls of rlog transformation
... Susan- Thank you for weighing in. I actually learned a good deal from your recently submitted paper, Waste Not, Want Not:Why rarefying microbiome data is inadmissible, available on Joey McMurdie’s website (for anyone else interested). Reading that manuscript is actually what turned me on to using D ...
written 5.9 years ago by Kristina M Fontanez220
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DESeq2 pitfalls of rlog transformation
... Dear Bioconductors- After previous discussions on this list, I had settled on using regularized log transformed counts in order to present relative abundance heatmaps/barcharts of my metagenomic data. As this transformation accounts for both differing library sizes and stabilizes the variance among ...
written 5.9 years ago by Kristina M Fontanez220
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Comment: C: genefilter kOverA filter by range
... Hi Jim- Thank you so much for your help. Your first solution worked for me and I’ve now captured the minimum and maximum log2fold changes in the new LFC3truenames object. > filtest<-rowSums(abs(otu_table(comp))>3)>0 > LFC3truenames=prune_taxa(filtest,comp) > LFC3truenames phylose ...
written 5.9 years ago by Kristina M Fontanez220
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Comment: C: genefilter kOverA filter by range
... Hi James, Unfortunately, your proposed solution didn’t work for me. I think it’s because I am working with objects built with the phyloseq package which I am trying to subsequently filter with the genefilter functions. First, a review of the two phyloseq objects from my last post: > comp phylos ...
written 5.9 years ago by Kristina M Fontanez220
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genefilter kOverA filter by range
... Dear Bioconductors, I am trying to use the genefilter package to filter a set of Log2fold changes so that I can keep those taxa with Log2fold changes > 3. However, the data itself consists of both positive and negative values, as is the case with log 2 fold comparisons. Example data: OTU Table: ...
genefilter written 5.9 years ago by Kristina M Fontanez220 • updated 5.9 years ago by James W. MacDonald52k
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Comment: C: Error installing development version of DESeq2
... Steve- Thank you for your help with this issue. Your last post solved my problems with the errors and I now have R 3.0 and R 3.1 installed side by side on my system. I’m sorry for the late reply as I was away over the weekend. Thanks again, Kristina ----------------------------------------------- ...
written 5.9 years ago by Kristina M Fontanez220
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Comment: C: Error installing development version of DESeq2
... Hi Steve- Thanks for the help. I deleted the development and corrupted release versions of R from my computer. Then, I downloaded the release version. Next, I renamed the release version in my Applications folder to R_3.0. Then I downloaded the installer package from att.com for the development ver ...
written 5.9 years ago by Kristina M Fontanez220
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Comment: C: Error installing development version of DESeq2
... Hi Steve- Unfortunately, your e-mail came about 10 minutes too late for me. I did indeed destroy my old version (3.0) of R. I did use the R-devel*.pkg available at att.com but I must have missed the installer prompt that prevented it from killing my current release install. Do you have any advice ...
written 5.9 years ago by Kristina M Fontanez220
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Comment: C: Error installing development version of DESeq2
... Dan- Thank you for that insight. I downloaded the development version and kept around my stable 3.0 version as well. I was then able to successfully download the development version of DESeq. Although, I am nervous about encountering the “Unsuffered Consequences” promised in the title. Thanks! Kr ...
written 5.9 years ago by Kristina M Fontanez220

Latest awards to Kristina M Fontanez

Great Question 5.9 years ago, created a question with more than 5,000 views. For DESeq2 pitfalls of rlog transformation
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Error installing development version of DESeq2
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Error installing development version of DESeq2

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