User: audrey

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audrey280
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Posts by audrey

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Bioinformatics Post doc position at UCSF
... Dear list, Here is a job advertisement posted on behalf of Owen Solberg and Prescott Woodruff. If you are interested, please contact Prescott.woodruff at ucsf.edu. Post-Doctoral Position in Applied Bioinformatics University of California, San Francisco The Woodruff Laboratory of the UCSF Airway C ...
mirna microarray qpcr written 9.9 years ago by audrey280
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Answer: A: QCparameters for Human Exon arrays (arrayQualityMetrics)
... Hi Gard, Sorry for the delay answering. I do not have much experience using arrayQualityMetrics for Exon arrays, so I have talked with Crispin Miller (simpleaffy package) about it and according to him "most of the Affymetrix QC metrics for the 3' IVT arrays aren't directly applicable to the exon ar ...
written 10.1 years ago by audrey280
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Answer: A: problem with arrayQualityMetrics
... Hi Joern, Thank you for your feedback. You are using the development version 2.5.2 and I have recently added legend on the RNA Degradation plot of this version, apparently I need to correct it. The release version 2.4.2 should not have this problem. Best wishes, Audrey > Hello, > > I ...
written 10.1 years ago by audrey280
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Answer: A: ArrayExpress error attaching phenodata
... Hi Paul, I am sorry for the delay replying. Indeed, usually in the sdrf file there is only one line per array which is why this particular dataset was causing an error. It has two lines per array, each line corresponding to a channel. What you can do is downloading the data using the getAE() functi ...
written 10.1 years ago by audrey280
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Answer: A: ArrayExpress
... Hi Colin, You can use the two functions getAE (to download the data) and subsequently the function magetab2bioc (please have a look at the help and vignette) from the ArrayExpress package. The ArrayExpress function is a wrapper for these two functions so the two outputs will be the same. If you wan ...
written 10.1 years ago by audrey280
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Answer: A: ArrayQualityMetrics: Problem with labels in plots. A bug??
... Hi Lohith, Thank you for your feedback and suggestions. It is true that spatial distributions require a large memory and cause the function to fail on some machines (note that with large memory it is most of the time possible to run it without problems). This is why I added an argument "spatial" th ...
written 10.1 years ago by audrey280
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Answer: A: ArrayQualityMetrics: Problem with labels in plots
... Hi Elliott, I did not manage to reproduce the error you got, so I have a few questions. Is the object rg an RGList? Does it have 4 channels (red foreground and background and green foreground and background)? Can you show how you go from rg to ma? Hopefully I will be able to understand better what ...
written 10.1 years ago by audrey280
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Comment: C: ArrayQualityMetrics: Problem with labels in plots. A bug??
... Dear Jeremy, Sorry I did not think about this, I think it takes a couple of days between the moment the developer modifies the version of the package and the moment you can actually install it using biocLite. You should be able to install version 2.4.1 after the week-end. Best wishes, Audrey jere ...
written 10.1 years ago by audrey280
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Answer: A: ArrayQualityMetrics: Problem with labels in plots. A bug??
... Dear Jeremy, Thank you for reporting this. You were right there was a problem in the code for the ordering of the colours. I have now corrected it, so arrayQualityMetrics version 2.4.1 should be working fine. Please let me know if you keep experiencing problems. Best wishes, Audrey jeremy wilson ...
written 10.1 years ago by audrey280
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Answer: A: Array express looking in wrong place for file...
... Hi Paul, I apologize for the delay in replying. The ArrayExpress database has been completely regenerated two weeks ago and some changes (like the naming of the zip files) needed some time to get synchronized with the Bioconductor package (especially because I was away at the same moment). The pro ...
written 10.1 years ago by audrey280

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