User: newmanss

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newmanss0
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Posts by newmanss

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phyloseq heatmap blank after multiple package updates
... Hello, After updating multiple packages, my phyloseq heatmaps are blank.  I have tried running previously run analyses that worked and running using older package versions but I have been unable to isolate the problem.  The heatmap is drawn and it is labeled correctly but the heatmap itself is gray ...
phyloseq heatmap written 12 months ago by newmanss0 • updated 12 months ago by Wolfgang Huber13k
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phyloseq biom json format conversion needed to hdf5 format for qiime
... Hi, I have analyzed my metagenome data with phyloseq and used the R package biom to output a biom file containing my phyloseq normalized and filtered data.  I need to run a statistical test in Qiime.  My biom file generates an error that appears to be a column name problem for 'id'.  As best I can ...
phyloseq hdf5 qiime biom json written 23 months ago by newmanss0 • updated 22 months ago by Bernd Fischer540
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Comment: C: phyloseq merge_samples attempt to set rownames on an object with no dimensions
... Update:  I ran the command using a larger number of samples.  Problem solved. ...
written 24 months ago by newmanss0
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phyloseq merge_samples attempt to set rownames on an object with no dimensions
... Hi,  I cannot resolve the source of this error when I attempt to merge samples using phyloseq.  The command is: > phymerge <- merge_samples(physeq, "expvar") Error in `rownames<-`(`*tmp*`, value = c("PBRC_LR_BM4218", "PBRC_LR_BM4787",  :   attempt to set 'rownames' on an object with ...
phyloseq error rownames merge_samples written 24 months ago by newmanss0
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Comment: C: DESeq2 design model-mothers & offspring timepoint comparisons
... Many thanks for your patient replies. ...
written 3.0 years ago by newmanss0
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Comment: C: DESeq2 design model-mothers & offspring timepoint comparisons
... So this design runs without error. [1] "Intercept" "Gender_M_vs_F" "Kinship_49_vs_47" [4] "Kinship_56_vs_47" "Kinship_57_vs_47" "Kinship_60_vs_47" [7] "Group_post_vs_offspring" "Group_pre_vs_offspring" "Group_preg_vs_offspring" What is the code ...
written 3.0 years ago by newmanss0
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Comment: C: DESeq2 design model-mothers & offspring timepoint comparisons
... It appears that the source of the design problem is the presence of males only in the offspring group?  Here is the restructured design as requested. This works: dds <- DESeq(DESeqTable, betaPrior = FALSE) resultsNames (dds) [1] "Intercept" "Kinship_42_vs_41" "Kinship_ ...
written 3.1 years ago by newmanss0
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DESeq2 design model-mothers & offspring timepoint comparisons
... Hello, I cannot seem to structure my model.matrix properly.  I would be very grateful for your assistance.  I have tried to follow the protocol outlined in these Bioconductor posts, https://support.bioconductor.org/p/61801/ and https://support.bioconductor.org/p/61801/ .  This a metagenome dataset ...
deseq2 design and contrast matrix multiple factor design model.matrix written 3.1 years ago by newmanss0 • updated 3.1 years ago by Michael Love19k
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Comment: C: DESeq2 design matrix for normal & enriched samples
... Many thanks for your detailed answer.  I'm looking forward to seeing the result. Susan ...
written 3.4 years ago by newmanss0
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Comment: C: DESeq2 design matrix for normal & enriched samples
... I am looking for differential expression in the enriched samples due to treatment after normalizing (adjusting?)  for the enrichment.  I have tried using FC ratios from DESeq2 run for each condition individually using enriched vs unenriched (IP/Input) for the contrast.  The resulting fold change wou ...
written 3.4 years ago by newmanss0

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Popular Question 23 months ago, created a question with more than 1,000 views. For DESeq2 design model for treatment analysis controlling for age and sex

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