User: ap3637

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ap36370
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Posts by ap3637

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Is there a data package containing complex RNA-Seq data?
... Does anyone know if there is a good RNA-Seq data set that is reasonably large and has multiple factors included in its metadata? For instance, the airway data set mentioned here, http://www.bioconductor.org/help/workflows/rnaseqGene/#starting-from-count-matrices , is nicely formatted for what I hop ...
deseq2 rnaseqgene airway rangedsummarizedexperiment rnaseqdataset written 5 weeks ago by ap36370 • updated 5 weeks ago by mario.zanfardino10
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Comment: C: DESeq failure after update: unable to find an inherited method for function mcol
... I seem to have resolved it, though I'm not sure exactly why. I updated devtools and roxygen packages and it seems to work again for some reason.   ...
written 6 months ago by ap36370
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Comment: C: DESeq failure after update: unable to find an inherited method for function mcol
... I get the following.  Shows 0 columns when i do this, but the dds shows 313.   This is really strange. > mcols(dds) DataFrame with 58233 rows and 0 columns ...
written 6 months ago by ap36370
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DESeq failure after update: unable to find an inherited method for function mcols for signature Rle
... I'm running DESeq2 and just updated all of my packages.  Now suddenly I can't run several DESeq functions, rlog, varianceStabilizingTransformation, and DESeq functions now all throw this error.     Here is my session info:   > sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-apple ...
deseq deseq2 R version compatibility written 6 months ago by ap36370 • updated 6 months ago by Michael Love17k
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Comment: C: What causes this DESeq2 error at "fitting model and testing"?
... Ok great, that's good to know.  So assuming the "estimating dispersions" goes through, for future reference for anyone who encounters this problem, try VST instead of rlog, and update your R packages.   My guess is that the rlog might have failed somehow in the larger data set, if I had to guess wh ...
written 6 months ago by ap36370
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Comment: C: What causes this DESeq2 error at "fitting model and testing"?
... Update: It seems like it's getting past this phase using VST and updated R packages.  At "estimating dispersions" now, so hopefully everything will go through. I did receive the following warning, but maybe it's okay.   27 rows did not converge in beta, labelled in mcols(object)$betaConv. Use lar ...
written 6 months ago by ap36370
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Comment: C: What causes this DESeq2 error at "fitting model and testing"?
... Thanks for your reply.  The output you requested is too many characters to post here directly, so here is a link to that information. https://justpaste.it/1c00t   Thanks very much for your help, the point about the releveling is also very useful.  I'm going to try to update some packages that are ...
written 6 months ago by ap36370
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Comment: C: What causes this DESeq2 error at "fitting model and testing"?
... Yes, using version 1.16. ...
written 6 months ago by ap36370
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What causes this DESeq2 error at "fitting model and testing"?
... I am using DESeq2 on a pretty large dataset.  I have mock and infection conditions for several mouse lines at 3 time points.  My goal is to contrast each line at each timepoint with it's corresponding mock at the same timepoint.  Previously I split the data into smaller subsets by line, but now I'm ...
deseq2 error differential expression written 6 months ago by ap36370
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Comment: C: DESeq2 design matrix with a single mock and multiple timepoints
... Thanks for your reply Michael.  This is really helpful.  I actually had tried this before using the composite column, Virus_Time, in the data file I provided.  I had believed that it wasn't the right thing to do because the resultsNames(dds) seemed pretty random, but it turns out I had not re-levele ...
written 8 months ago by ap36370

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