User: Florence Cavalli

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Posts by Florence Cavalli

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Answer: A: Specond with R 3.2.2
... Hello Meeta, Could you send me directly a small example dataset that would allow me to reproduce the error.  Thanks, Florence ...
written 3.5 years ago by Florence Cavalli50
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Questions regarding 'specond' r-program library package
... Dear Mousami, Thanks for your email and interest in the SpeCond package. You don't need to worry about the above warnings. These warnings are returned by the mclust package that the SpeCond method uses to fit a mixture of normal distribution. I restricted the number of normal (or component) to be ...
kidney lung prostate probe specond written 5.3 years ago by Florence Cavalli50
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Comment: C: 450k annotation packages compatible version and analysis with blockFinder (minfi
... Thank you very much for your quick answers and looking in detail into this as well as updating the package. The updateObject(OBJECT) function works perfectly ! :-) Yes the corrected design matrix makes sense. I was really exploring and did not fully understand how blockfinder worked yet. Will look ...
written 5.4 years ago by Florence Cavalli50
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450k annotation packages compatible version and analysis with blockFinder (minfi)
... Hello, I am working with 450k methylation data. - Is there a way to modify the annotation linked to an MethylSet object, (or is this something we are not supposed to do)? I created my large MethylSet object under the pervious version of R and Bioc and at the time the annotation package IlluminaHum ...
annotation clustering convert minfi written 5.4 years ago by Florence Cavalli50 • updated 5.4 years ago by Kasper Daniel Hansen6.4k
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Comment: C: IlluminaHumanMethylation450kprobe for nearest TSS calculation question
... Hello, I looked at this code as well and I would have two comments about it. To get the closest TSS, I understand why we use precede() and the fact that the argument ignore.strand is by default as FALSE (for GRanges object, which is a good thing), so the strand of the gene is taken into account. Ho ...
written 6.1 years ago by Florence Cavalli50
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Answer: A: identifying consistently expressed genes between replicates
... Hi Wendy, Depending on your number of cell types, you can try the SpeCond package for your analysis. It allows to detect condition-specific gene expression, in your case cell-type specific gene expression. Let me know if you have any questions about it. Best, Florence 2011/4/10 Wendy Qiao > H ...
written 8.0 years ago by Florence Cavalli50

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Popular Question 3.5 years ago, created a question with more than 1,000 views. For 450k annotation packages compatible version and analysis with blockFinder (minfi)

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