User: Biorunner88

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Biorunner8810
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Spain
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Posts by Biorunner88

<prev • 25 results • page 2 of 3 • next >
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Comment: C: loadGSC() Piano package
... Thanks. I've already read the manual. I believe I'm just going to need the gene onotoly gene set. I'll try to use the org.Sc.sgd.db package to get the GO in order to create the data.frame needed for this function.   Thanks again. ...
written 2.5 years ago by Biorunner8810
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loadGSC() Piano package
... Hi. I've use limma and I want to use the output of toptable with the piano package. I'm having a problem with the function loadGSC() because I'm not really sure the input file (it's a gene set). My data comes from Saccharomyces cervisiae, the genes are in systematic name, I've cheked in here http ...
piano written 2.5 years ago by Biorunner8810 • updated 2.5 years ago by Leif Väremo60
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Answer: A: Filtering genes for GOstats
... Still getting some errors, this time is when I run the hyperGTest. Alk.entrezid <- select(org.Sc.sgd.db, alk_names, "ENTREZID") #New fashioned way anyDuplicated(Alk.entrezid$ENTREZID) dim(Alk.entrezid) #Removing duplicated -mainly NA in ENTREZID column- Alk.entrezid <- as.character(Alk.entr ...
written 2.6 years ago by Biorunner8810
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Comment: C: Filtering genes for GOstats
... Thanks, I was using the wrong function and I was doing it the wrong way. ...
written 2.6 years ago by Biorunner8810
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Comment: C: Filtering genes for GOstats
... Thanks I solved it the old fashioned way, and I've noticed that if you do it the old way yo get duplicated, meanwhile if you do it the new way you get non duplicated. ...
written 2.6 years ago by Biorunner8810
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Answer: A: Filtering genes for GOstats
... I'm trying to create the universeGeneIds Alk.entrezid <- unlist(mget(alk_names, org.Sc.sgdENTREZID)) Where alk_names is a list of genes present in my array that at least have one expression value, so all genes with NA in it's row are removed. But I get the following error: Error en unlist(m ...
written 2.6 years ago by Biorunner8810
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Comment: C: Filtering genes for GOstats
... I have understood that your universe of genes (geneIds, the ones you analyzed from your experiment and are statiscally significative) , should match the universe of genes (universeGeneIds) so the statistics work properly. In this case the universe is the whole universe of gene from Yeast, instead o ...
written 2.6 years ago by Biorunner8810
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Filtering genes for GOstats
... Hi I'm using GOstats, I've created the universe for the Saccharomyces cerevisiae frame <- toTable(org.Sc.sgdGO) goframeData <- data.frame(frame$go_id, frame$Evidence, frame$systematic_name) goFrame <- GOFrame(goframeData, organism = "Saccharomyces cerevisiae") goAllFrame <- GOAllFram ...
gostats written 2.6 years ago by Biorunner8810
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Comment: C: Limma linear models
... Thanks! Other question related to this. I have filtered the output of toptable. In this case I filtered genes with p.value lower than 0,05 and genes with t value > than 0 and t value < 0, in order to obtain upregulating genes(t > 0) or downreagulatin genes(t < 0). But when I plot some ...
written 2.6 years ago by Biorunner8810
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Comment: C: Limma linear models
... The eBayes should be donde with the output of lmFit instead of with the alk_set. I guess that is a mistake. I'm working with Saccharomyces cerevisiae and the genes are in systematic gene names (ex: YDL229W). I still need to dig in how ebayes it's working in this case. I know how the package has be ...
written 2.7 years ago by Biorunner8810

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