User: Jason Skelton

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Jason Skelton510
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Posts by Jason Skelton

<prev • 51 results • page 1 of 6 • next >
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gls.series and mrlm
... Hi Is is possible for mrlm in limma to treat duplicates the same way as gls.series does ? I.e using consensus correlation We have tried implementing this in our group ourselves but with no success thus far. Is there any reasons why this would not be good idea ? Any info greatfully received Cheer ...
limma written 14.4 years ago by Jason Skelton510
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Calculating confidence intervals
... Hi everyone Is it possible to calculate confidence intervals for each gene after linear model fitting with limma ? Many thanks Jason -- -------------------------------- Jason Skelton Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1SA Tel +44(0)1223 834244 Ext 7123 Fa ...
limma written 14.4 years ago by Jason Skelton510
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limma stdev.unscaled
... Hi I wanted to calculate coefficients of variation for some genes using data analysed with limma (two-colour microarray data), and found that the SD for all genes in each comparison were the same e.g. from fit$stdev.unscaled Comparsion 1 Comparison 2 Comparison 3 Min. :0.5599 Min ...
microarray written 14.4 years ago by Jason Skelton510
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Modelmatrix
... You're not using the 'parameters' argument to modelMatrix() correctly. The main point though is that there is no need to take special action to allow for different numbers of replicates. This is accommodated automatically in the course of an ordinary analysis. Gordon Dear Gordon, Sorry for bein ...
written 14.6 years ago by Jason Skelton510
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modelMatrix question
... Hi I have a question regarding the modelMatrix function in limma. Which has been covered before however I haven't found an appropriate answer in the documentation or the list archives. Can one use modelMatrix to adjust for unequal numbers of technical replicates? To take a very simplified example f ...
limma written 14.6 years ago by Jason Skelton510 • updated 14.6 years ago by Gordon Smyth39k
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Answer: A: spotSegmentation
... Hi I'm attempting to use the spotSegmentation package and I've run the demo using the dataset provided with the package with no problems. However its not clear how to use your own images which I'm presuming will be tiff images for each channel ? Also after you have used the spotseg function you can ...
written 14.6 years ago by Jason Skelton510
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spotSegmentation
... Hi I'm attempting to use the spotSegmentation package and I've run the demo using the dataset provided with the package with no problems. However its not clear how to use your own images which I'm presuming will be tiff images for each channel ? Also after you have used the spotseg function you can ...
limma spotsegmentation written 14.6 years ago by Jason Skelton510
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Spot quantitation
... Hi I was wondering if anyone has any opinions about the SPOT spotfinding software from csiro (I.e the package that runs in R) and it's limitations, benefits, opinion about batch performance accuracy etc. Has anyone done any direct comparisons of SPOT with Genepix or other spotfinding software avali ...
limma written 14.6 years ago by Jason Skelton510
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random location of duplicate spots and use of limma
... > > >Hello > >There are approximately 6000 different genes on the arrays, there are two spots for each gene >The duplicated spots have random location, which means that the number of spots between each duplicate is not the same for every gene. This is the summary for the distances: ...
limma written 14.9 years ago by Jason Skelton510
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accessing decideTests Info
... Hi all I have the following data that I'd like to further explore from decideTests > summary(DTresults) Germball Cerc TwoDay SevenDay TwentyOneDay AdultWorm Egg -1 1035 868 764 561 706 415 826 0 4891 5057 5144 5520 5178 5573 5150 1 602 ...
written 15.1 years ago by Jason Skelton510

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