User: muc345

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muc3450
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Posts by muc345

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Comment: C: DESeq help for comparing contrasts
... Michael, I finally got around the fixing all of my packages. Once I had updated versions and the output from BiocManager::valid() was "TRUE", the code worked! Thank you for your help! ...
written 6 months ago by muc3450
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Comment: C: DESeq help for comparing contrasts
... I was hoping that would work, too. But I still get the Line1/2/3 issue. :( ...
written 6 months ago by muc3450
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Comment: C: DESeq help for comparing contrasts
... Michael, I'm working on this now. I keep running into this issue: BiocManager::install(c( "expm", "phangorn", "RcppArmadillo" ), update = TRUE, ask = FALSE) more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date Warning message: 3 packages out-of-date; 0 packages to ...
written 6 months ago by muc3450
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Comment: C: DESeq help for comparing contrasts
... [82] magrittr_1.5 data.table_1.12.0 gmodels_2.18.1 [85] mvtnorm_1.0-10 pkgload_1.0.2 hms_0.4.2 [88] mime_0.6 xtable_1.8-3 pbkrtest_0.4-7 [91] XML_3.98-1.19 gridExtra_2.3 compiler_3.5.1 ...
written 6 months ago by muc3450
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Comment: C: DESeq help for comparing contrasts
... Here is my output: > BiocManager::valid() * sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Ve ...
written 6 months ago by muc3450
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Comment: C: DESeq help for comparing contrasts
... Hi Michael, Thanks for the response. Here is what I'm seeing: > diagdds <- DESeq(line.ds, test="Wald", fitType="parametric") estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing > ...
written 6 months ago by muc3450
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DESeq help for comparing contrasts
... Hello there, My issue is that DESeq no longer works and does not give me the correct contrast options. This was working before I updated to DESeq2 1.22.2 Here is my code: ``` > line.ds <- phyloseq_to_deseq2(ps.phyla, ~ Line) > diagdds <- DESeq(line.ds, test="Wald", fitType="parametri ...
deseq2 written 6 months ago by muc3450 • updated 6 months ago by Michael Love25k

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