User: Helen Smith

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Helen Smith100
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h************@manchester.ac.uk

Posts by Helen Smith

<prev • 10 results • page 1 of 1 • next >
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correlation analysis
... Hi All, I have a general bioconductor question. I've been struggling with how to do this all week, so any help would be much appreciated, I have used correlation analysis in the past to define a range of genes which correlate with a certain prognosis score (all prognosis scores known). Please ...
written 5.6 years ago by Helen Smith100 • updated 5.6 years ago by Steve Lianoglou12k
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Comment: C: biogrid cytoscape plugin
... Yes I have. I just thought it might be worth asking the bioconductor people as I know a large percentage of use can use both...... Didn't mean to be a nuisance, just getting desperate. Kind regards, Helen -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: 03 February ...
written 5.6 years ago by Helen Smith100
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biogrid cytoscape plugin
... Hi All, I'm having a nightmare uploading the cytoscape plugin 'BioGrid' (version 2.2) into cytoscape (version 2.8.3). I keep getting the error message: unable to install plugin: java.langNullPointerException I have the up-to date version of java and can't see what the problem is........ Anyone els ...
written 5.6 years ago by Helen Smith100 • updated 5.6 years ago by Dan Tenenbaum8.2k
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upload multiple genelists at a time for GO or pathway enrichment
... Hi All, I have a list of clusters generated through biolayout which I need to annotate for GO annotations. I can do this one-by-one using DAVID etc but as there are 97 clusters this is a rather lengthy procedure. Do any of you know of any tools were you can upload multiple lists of genes to be ann ...
go cdf oligo pdinfobuilder xps written 5.9 years ago by Helen Smith100 • updated 5.9 years ago by Pekka Kohonen190
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Comment: C: limma - batch dates incorrporated into t-test
... Haha good point (my ghetto roots playing up again). I'll have a good look into the different stats I can produce using ebayes this weekend then. Random query: is there any way of predicting how well the batches have been corrected for? When I used to incorporate the batch dates into an ANOVA, if th ...
written 6.0 years ago by Helen Smith100
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Comment: C: limma - batch dates incorrporated into t-test
... That seems to have all worked perfectly thank you so much! Just to double check: my batch dates aren't a contrast but have been incorporated into the t-test as a factor using the following code after you contrast line: ###Contrast matrix### contrast <- makeContrasts(oocyte - four_cell,oocyte - e ...
written 6.0 years ago by Helen Smith100
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Comment: C: limma - batch dates incorrporated into t-test
... Thanks James, that all worked great apart from the last line: contrast <- makeContrasts(blastomere - oocyte, blastomere - eight_cell, blastomere - four_cell, , levels =design) Which produced the following error: Error in makeContrasts(oocyte - four_cell, oocyte - eight_cell, oocyte - : T ...
written 6.0 years ago by Helen Smith100
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limma - batch dates incorrporated into t-test
... Hi All, I am new to limma and R programming. I have the CEL.files uploaded, normalised as an expression set, and have put together the target.txt file containing the following layout: Name FileName Target Date 5 0207_DaB7_H_ea_Blast1.CEL blastocyst 13/02/2007 6 ...
limma written 6.0 years ago by Helen Smith100 • updated 6.0 years ago by James W. MacDonald51k
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Comment: C: Affy: probeset to gene expression with expresso
... Hi, Thank you Jim. Can I ask, I have always averaged the expressions and they completed pathway analysis for the genes rather than the probes. Do you consider it better to leave it as individual probes and assess individual expression at the pathway level? I'm torn as to which is the best approach ...
written 6.1 years ago by Helen Smith100
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take the average log fc for each gene
... Hi All. Apologies as I'm just getting to grips with R. I have a set of genes and log fold changes. As the genes have been converted from Affymetrix probes, and up to 11 probes represent one gene, I have a range of different log fold changes for each gene. I would like to take the average log fc fo ...
written 6.1 years ago by Helen Smith100 • updated 6.1 years ago by James W. MacDonald51k

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