User: Sanches

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Sanches0
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Posts by Sanches

<prev • 25 results • page 2 of 3 • next >
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Comment: C: Treat Method - number of DE genes
... Hi Gordon,  The software is working correctly.   You just answered my question. But If I set lfc=log2(1.5), I would increase false discovery rate, right? So, in your opinion, what is the best lfc cutoff? Thanks in advance.   ...
written 9 weeks ago by Sanches0
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Treat Method - number of DE genes
... Hello everybody,  I have been running my microarray data using limma and I'd like to ask a question. What is the best way to reduce the number of differentially expressed genes? As you can see below, I have used the treat method to reduce it and no differentially expressed genes were listed in the ...
treat method number of de genes written 9 weeks ago by Sanches0 • updated 8 weeks ago by Gordon Smyth32k
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Comment: C: Error in columns(org.Hs.eg.db) : could not find function "columns"
... Hi James,  Thanks for your help. I had loaded the package before using "columns". I  have found out the problem. Everything went well when I loaded the biomaR package. Thanks         ...
written 9 weeks ago by Sanches0
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Error in columns(org.Hs.eg.db) : could not find function "columns"
... Hi all,  I have been running an analysis from microarray data and when I try to run this line " columns(org.Hs.eg.db)", I get an error. Could anyone please help me to understand this problem?   source("https://bioconductor.org/biocLite.R") install.packages("org.Hs.eg.db", repos="http://bioconduc ...
annotation error message written 9 weeks ago by Sanches0 • updated 9 weeks ago by James W. MacDonald45k
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Filtering replicated genes
... Hi everybody, Let me ask you all a question. What is the better way to perform a filter from my microarray data?  If I use the UniProt ID to filter replicated genes, is it correct? Thanks in advances   ...
filtering genes written 9 weeks ago by Sanches0 • updated 9 weeks ago by Gordon Smyth32k
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Comment: C: Converting GeneBank Access number into Entrez gene IDs
... Thanks for your tip, James. I will check it. I have just tried it. I was not able to do that. I would like to convert SystematicName(GeneBank Access Number) into Entrez gene IDs. Could anyone help me?     > head(DE21)           Row  Col    ControlType     ProbeName       SystematicName         ...
written 10 weeks ago by Sanches0
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Converting GeneBank Access number into Entrez gene IDs
... Hi there,  I have been running two-color microarray data from Agilent and  I would like an advice to convert GeneBank Access number into  Entrez gene IDs? Cheers   ...
annotation written 10 weeks ago by Sanches0 • updated 10 weeks ago by James W. MacDonald45k
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Comment: C: Information about .GAL file from two-color channel microarray
... Dear Gordon,  You are right. I apologize for my lack of experience.  I have the following information:  . Spot ID  and GenBank Accession Number. How can I replace the GenBank Accession Number by Gene Name? Thanks in advance ...
written 10 weeks ago by Sanches0
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Information about .GAL file from two-color channel microarray
... Dear all,  Let me ask you a question. I have been analyzing a two-color microarray data but I do not have the .gal file. I tried to get this file from Agilent web site but I do not have the following information: Design ID and slide format. So, is there another possibility to get this information? ...
.gal file two-color microaray written 10 weeks ago by Sanches0 • updated 10 weeks ago by Gordon Smyth32k
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two-color microarray - Gene Set Enrichment Analysis
... Hello everybody, I would like to ask a question. What is the best package for Gene Set Enrichment Analysis using two-color channel microarray data? Could anyone suggest me a tutorial for it?   Thanks in advance.  ...
gsea twocolor microarray written 11 weeks ago by Sanches0 • updated 11 weeks ago by Gordon Smyth32k

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