User: Thomas Hampton

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Posts by Thomas Hampton

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Answer: A: Expected number of DE genes?
... Dear Jessica, The answer to this sort of question depends on the question you are actually asking. You no doubt know a) that in this sort of test many genes are expected to reach nominal significance by chance and b) that software packages include algorithms intended to differentiate between these ...
written 3.4 years ago by Thomas Hampton740
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RmiR and RmiR.Hs.miRNA
... Hello Group, I have great interest in comparing miRNA target predictions made by various algorithms. The RmiR.Hs.miRNA package appears to be a perfect solution, except, as far as I can tell, its data was collected in 2009, which is rather a long time ago in the history of miRNA. I suspect more curr ...
mirna rmir written 3.9 years ago by Thomas Hampton740
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Answer: A: GEOmetadb query to retrieve sample groups
... The following getGEO query retrieves data files and meta data for a recent GEO submission of mine, one that has been curated: GDS4252 <- getGEO("GDS4252") Columns(GDS4252) > str(Columns(GDS4252)) 'data.frame': 16 obs. of 4 variables: $ sample : Factor w/ 16 levels "GSM754979","G ...
written 4.5 years ago by Thomas Hampton740
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GEOmetadb query to retrieve sample groups
... The following getGEO query retrieves data files and meta data for a recent GEO submission of mine, one that has been curated: GDS4252 <- getGEO("GDS4252") Columns(GDS4252) > str(Columns(GDS4252)) 'data.frame': 16 obs. of 4 variables: $ sample : Factor w/ 16 levels "GSM754979","GSM ...
geometadb written 4.5 years ago by Thomas Hampton740 • updated 4.5 years ago by Sean Davis21k
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Comment: C: GEOquery and Sample Subsets
... This looks totally cool. Is there a place where one can view the schema of the relational db? In any case -- Thanks tons! Tom ________________________________________ From: seandavi@gmail.com [seandavi@gmail.com] on behalf of Sean Davis [sdavis2@mail.nih.gov] Sent: Tuesday, June 04, 2013 1:19 ...
written 4.5 years ago by Thomas Hampton740
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Comment: C: GEOquery and Sample Subsets
... Exactly! Thanks. ________________________________________ From: seandavi@gmail.com [seandavi@gmail.com] on behalf of Sean Davis [sdavis2@mail.nih.gov] Sent: Tuesday, June 04, 2013 12:54 PM To: Thomas H. Hampton Cc: bioconductor at r-project.org Subject: Re: [BioC] GEOquery and Sample Subsets On T ...
written 4.5 years ago by Thomas Hampton740
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GEOquery and Sample Subsets
... I am using to GEOquery to establish sample subsets of GEO data -- that is, I would like to know which samples are replicates. I am doing it something like this: gds505 <- getGEO("GDS505") Columns(gds505) > str(Columns(gds505)) 'data.frame': 17 obs. of 4 variables: $ sample : Factor ...
geoquery written 4.5 years ago by Thomas Hampton740 • updated 4.5 years ago by Sean Davis21k
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Answer: A: Analysis of Differentially Expressed Genes using Microarray Technology
... This is a great question. Obviously, with an N of 1, you are sorely limited in what you can say. In your consideration, you need to consider the ratio between your two samples, but you should also consider whether the ratio is based on a gene that is well-expressed in your system. Most genes are not ...
written 5.2 years ago by Thomas Hampton740
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Extracting PROBE_ID from lumiBatch
... The default featureName created by lumiR is a nuID. Is there some way to extract corresponding Illumina probe ids from a lumi batch? Thanks very much. Tom ...
probe written 5.9 years ago by Thomas Hampton740
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lumiR Does Not Create lumi Batch
... My attempt to create a lumi batch fails when I use a final report text file as input. The text file has the following columns: [1] "TargetID" "ProbeID" [3] "X6303230026_A.AVG_Signal" "X6303230026_A.Detection.Pval" [5] "X6303230026_B.AVG_Signal" "X6303230026_B.Detection. ...
lumi written 6.0 years ago by Thomas Hampton740 • updated 6.0 years ago by Sean Davis21k

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