User: A Gossner

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A Gossner50
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a********@ed.ac.uk

Posts by A Gossner

<prev • 8 results • page 1 of 1 • next >
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Comment: C: SystemPipeR GO term enrichment analysis - filterDEG
... CLID CLSZ GOID NodeSize SampleMatch Phyper Padj Term Ont GO_OL_Match 2815 M-C_up_down 179 GO:0006954 294 13 1.20E-05 0.001288505 inflammatory response BP 53 24071 M-C_up 121 GO:0006457 139 8 5.20E-0 ...
written 3.3 years ago by A Gossner50
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Comment: C: SystemPipeR GO term enrichment analysis - filterDEG
... Okay, Thank you.   ...
written 3.3 years ago by A Gossner50
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SystemPipeR GO term enrichment analysis - filterDEG
... Unsure what exactly the 'UporDown' value represents in terms of the differrentially expressed genes associated with the corresponding GO term. Does it represent the total number of genes up and down regulated (that pass the filter settings) for that specific GO term and if it so why do you get GO te ...
systempiper go term written 3.3 years ago by A Gossner50
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Answer: A: edgeR and FDR values always equals 1
... Mark Robinson writes: Hi Mark, > > Hi Anton. > > I've had a quick look at both batches of your plots. The replicates are quite variable, but something is > indeed unusual. Can you post your full set of commands used? > > Cheers, > Mark > Typically for this data just f ...
written 8.8 years ago by A Gossner50
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Answer: A: edgeR and FDR values always equals 1
... Hi Gordon, Gordon K Smyth writes: > Another curious fact is that all the putative differential expression is one > direction, down in the INF group. Have plotted the fold change smear plots and the top 500 DE tags seem to lie in a very strange line. Not sure what the cause/effect this is ...
written 8.8 years ago by A Gossner50
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Answer: A: edgeR and FDR values always equals 1
... Gordon K Smyth writes: > > Hi Anton, > > This is the way the software is designed to behave when there is no > differential expression between your groups. The software is telling you > that there is no statistically significant differential expression. > > The reason for ...
written 8.9 years ago by A Gossner50
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Comment: C: edgeR and FDR values always equals 1
... Hi Simon, Have plotted two samples as you suggested [ plot (d$counts[,2],d$counts[,3],log="xy")] and saved the file on the FTP server. ftp.ed.ac.uk Login using the username 'anonymous' and use your email address as password. get /edupload/logplot.eps as well as get /edupload/plot2.eps and get /edup ...
written 8.9 years ago by A Gossner50
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edgeR and FDR values always equals 1
... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ...
written 8.9 years ago by A Gossner50

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