Showing : qiime • reset
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DESeq2 intstallation error on fedora
deseq2 R fedora qiime
updated 3.1 years ago by 34k • written 3.1 years ago by • 0
1
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1
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688
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Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 3.8 years ago by 34k • written 3.8 years ago by • 0
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2
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550
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QIIME Differential abundance on multiple studies
deseq2 qiime
updated 4.0 years ago by 34k • written 4.0 years ago by • 0
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1.6k
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QIIME, R and bioconducter
R qiime
updated 4.5 years ago by 58k • written 4.5 years ago by • 0
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1.1k
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phyloseq biom json format conversion needed to hdf5 format for qiime
biom json hdf5 qiime phyloseq
updated 4.9 years ago by ▴ 540 • written 4.9 years ago by • 0
2
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889
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Metagenome seq errors using biom (1.3) file
metagenomeseq qiime biom
updated 5.1 years ago by ▴ 280 • written 5.1 years ago by • 0
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16k
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Error in file(con, “r”) : cannot open the connection
r phyloseq import_biom otu qiime
updated 5.9 years ago by ▴ 20 • written 5.9 years ago by • 0
7 results • Page 1 of 1
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Answer: Error in makeTxDbFromGFF(txomeInfo$gtf) by Michael Love 34k
I see that tximeta found a linked transcriptome. Can you show this part of your code as well? How did you create the `linkedTxome`?
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Gordon Smyth 43k
You need to start by doing an ordinary paired analysis.
Comment: Recalculated abundance data output table with DEseq2 by Michael Love 34k
Yes, DESeq() then results(). When you print the table it will say MLE. No we don’t have a function to do that.
Comment: Recalculated abundance data output table with DEseq2 by michael.morash • 0
Thanks for getting back to me so quickly. The final comparison we are looking to report are the effects of filtering out low count genes us…
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Field -Ye • 0
Hi Professor Smyth, Thank you for pointing me to your previous publication. I went through the verbal part and found you did pursue the DG…
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Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
Error in .rowNamesDF<-(x, value = value) :duplicate row.names are not allowed DESeq2
Comment: How to build a GRangesList where each GRanges element is a CDS coordinate of gen
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