User: noushin.farnoud

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Posts by noushin.farnoud

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Comment: C: Error with Reporting Tool and DESeq2
... Thanks Jamess! Above, I had increased the p-value cutoff for the "temp" subset to 0.1 just in case that was the cause. It seems even 0.1 was not large enough and when I increased it to 1, in fact it published the results successfully. As you said what was confusing me was the "error msg". ...
written 4.6 years ago by noushin.farnoud0
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Comment: C: HTMLReport of DESeq2 results with Ensembl Gene Ids
... I don't see why this would bring confusion! I have not yet received a working answer on this. That reply was a link to a post that I had seen and tried before posting my question. It does not work if not all Ensembl genes have a unique corresponding Entrez id (which happens to be my case!).  Publish ...
written 4.6 years ago by noushin.farnoud0
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Error with Reporting Tool and DESeq2
... Hi All,                          I can not publish the report for only a "subset" of  genes in DESeqDataSet, while the original DeseqtDataSet can be published without any problem. I can not figure why this happens. For example: library(DESeq2) library(ReportingTools) data(mockRnaSeqData) conditi ...
deseq2 publish written 4.6 years ago by noushin.farnoud0 • updated 4.6 years ago by James W. MacDonald50k
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HTMLReport of DESeq2 results with Ensembl Gene Ids
... Hello All, I would like to generate an HTML report from DESeq2 results of RNASeq analysis. I have followed the example in the ReportingTool documentation and have no problem with that, but unlike that example my deseq result dataset does not have Entrez IDs and instead it has Ensembl IDs. And I hav ...
reportingtools deseq2 publish written 4.7 years ago by noushin.farnoud0 • updated 4.4 years ago by Federico Marini120

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Popular Question 3.8 years ago, created a question with more than 1,000 views. For HTMLReport of DESeq2 results with Ensembl Gene Ids

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