User: SamGG
SamGG • 160
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- 3 weeks, 6 days ago
- Joined:
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Posts by SamGG
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... I agree Gordon's comment: use limma but not voom because spectrometer are not counting values but measuring the are of a peak. Imputation of missing is a major point. Missing values are not at random but mainly occur because the intensity of the peak is too low to be captured by the spectrometer. Mo ...
written 27 days ago by
SamGG • 160
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... You have to store the result in a variable, then you can access it.
res.split <- split(singlets, peaks)
res.split$`area 2`
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written 9 weeks ago by
SamGG • 160
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... For an extensive example, take a look at the function cytof_addToFCS of cytofkit
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written 10 weeks ago by
SamGG • 160
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Comment:
C: GSEA for RNA-seq analysis
... Dear Gordon,
Without wasting too much time, could you provide an easily comprehensible reference about "p-value correction algorithm can't work with permutation methods"? I am wondering if this applies to the SAM methodology.
Sorry for being out of the scope of the OP.
...
written 3 months ago by
SamGG • 160
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... Hi,
Something went wrong during the installation of flowCore. You need to solve all the dependencies that flowCore will complain about. For example, you should install the mvtnorm package, either using install.packages("mvtnorm") or BiocInstaller::biocLite("mvtnorm"). Then try again library(flowCor ...
written 4 months ago by
SamGG • 160
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... May be you scan and/or share the header of both files. I suspect something like the number of bits par data point.
hd = flowCore::read.FCSheader(files = file.name)
write.csv(hd[[1]], "before.csv")
...
written 5 months ago by
SamGG • 160
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Comment:
C: Beginner & HowTo-flowCore-Example
... Hi,
Your sessionInfo() sounds up to date (at least the same as mine). Next time, please do add missing information as a comment of your original question.
In order to track the error, you should check the content of fcsfiles or simply run the following command
list.files(pattern = "CytoTrol", sy ...
written 5 months ago by
SamGG • 160
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... Hi,
I looked at flowcore's code (IO.R file). Datasets are identified using the $NEXTDATA keyword. If there is none, there is only one dataset in the FCS file. So load the TEXT segment of the FCS file using read.FCSheader() and find any $NEXTDATA keyword using grep. To go further take a look at the ...
written 5 months ago by
SamGG • 160
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... Hi Samuel.
I don't have an answer. I already did some test using OMIP018 and this function was OK with the parameters you used. Look at my tests at http://rpubs.com/SamGG/spillover-omip-018 and issue IMHO concerning the row normalization https://github.com/RGLab/flowCore/issues/94
I encouraged you ...
written 8 months ago by
SamGG • 160
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... No doubt limma is perfect. GeneAnova does seem to compute a standard ANOVA and does not seem to manage false discovery rate. IMHO, this makes a big difference.
You can increase the FDR threshold up to 20%, but there is chance that the differences in your experiment are not related to the PHENO para ...
written 8 months ago by
SamGG • 160
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For A: Problem with HDF5 and ncdfFlow
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