User: ap3637

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ap36370
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Posts by ap3637

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Comment: C: Why does biomart work on humans and not mouse genes for HGNC symbol conversion?
... Thanks very much, you're right on the money! ...
written 8 months ago by ap36370
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Why does biomart work on humans and not mouse genes for HGNC symbol conversion?
... I am trying to use biomart for some ID mapping between humans and mice.  I have a couple of sets of genes I'm interested in and want to bring the IDs into a common space by mapping both gene ID sets to their corresponding HGNC symbol.   > head(human_de_geneIDs) [1] "ENSG00000175518" "ENSG0000023 ...
biomart R homologue written 8 months ago by ap36370 • updated 8 months ago by swbarnes2170
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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 14 months ago by ap36370 • updated 14 months ago by mario.zanfardino150
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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 19 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 19 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 19 months ago by ap36370 • updated 19 months ago by Michael Love23k
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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 19 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 19 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 19 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 19 months ago by ap36370

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