User: emiliomastriani

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Posts by emiliomastriani

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Calulation of ka/ks (dn/ds) using sliding windows
... Hello guys, I wish to do the same calculation like https://www.mathworks.com/examples/bioinfo/mw/bioinfo_product-dndsdemo-analyzing-synonymous-and-nonsynonymous-substitution-rates (calulation of ka/ks (dn/ds) through sliding windows) using Bioconductor. Is there some package that can support my rese ...
evolutionary analysis written 29 days ago by emiliomastriani0
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ReactomPA error using viewPathway
... Hello I tried to use the ReactomePA package and everything looks good, but finally I got the following error:   > viewPathway("E2F mediated regulation of DNA replication", readable=TRUE, foldChange=CL5_geneList) 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 ...
reactomepa reactome bioconductor viewpathway written 10 months ago by emiliomastriani0 • updated 10 months ago by Guangchuang Yu800
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categories can not be recognized in Bioconductor/GeneAnswers
... Hello guys, I hope that someone of you can help me.  I just finished my analysis of an Illumina microarray using beadarray. I got all information that I need to start my "concept" investigation using GeneAnswers (it's not the first time that I use it). Something it's not right. It looks that some/ ...
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beadarray error conversion
... Dear guys, after a long job I got my limmaRes as result of limmaDE analysis, as you can see from the next: str(limmaRes) Formal class 'limmaResults' [package "beadarray"] with 11 slots ..@ DesignMatrix : num [1:16, 1:2] 0 0 0 0 0 0 1 1 1 1 ... .. ..- attr(*, "dimnames")=List of 2 .. .. ...
beadarray limmaresults expressionset as pdata annotateddataframe written 11 months ago by emiliomastriani0 • updated 11 months ago by Gordon Smyth32k
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Answer: A: beadarray error importing from GEOquery
... Dear Mark, thank you very much for your support. I applied your update, but I am afraid that something is not right. Going to check the validity of the created object I get the following error:   > validObject(summaryData) Error in validObject(summaryData) : invalid class “ExpressionSetIll ...
written 11 months ago by emiliomastriani0
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Answer: A: beadarray error importing from GEOquery
... Thank you very much for your support.  I am sure that you will give soon an optimal solution to the problem. In the meantime, any other suggestions are welcome!!!!   Best regards, Emilio   ...
written 11 months ago by emiliomastriani0
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beadarray error importing from GEOquery
... Hello guys, I need your support in order to understand how to solve my problem, because I already spent too much time and I don't know how to solve it. The steps done are the following (as in vignette of beadarray): > source("http://www.bioconductor.org/biocLite.R") Bioconductor version 3.4 (B ...
geoquery beadarray expressionsetillumina getgeo written 11 months ago by emiliomastriani0 • updated 11 months ago by Gordon Smyth32k

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