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User: SamGG
SamGG • 170
- Reputation:
- 170
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- Trusted
- Location:
- France
- Last seen:
- 1 month ago
- Joined:
- 4 years, 11 months ago
- Email:
- s***************@inserm.fr
Posts by SamGG
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... Hi,
With R3.5.2, you should use the new installer delivered by the BiocManager package. More on that https://bioconductor.org/install/.
The MSnbase is a dependency of RforProteomics, so no need to install it separately.
> BiocManager::install("RforProteomics")
Bioconductor version 3.8 (B ...
written 4 weeks ago by
SamGG • 170
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... Hi,
I don't suspect a memory limit there. The read.FCS has been extended recently to cope with file bigger than 2GB. The error sounds like a problem in reading and interpreting the TEXT segment of the FCS file. Of course reading a CSV file avoids this problem because there is no such meta data. I t ...
written 4 weeks ago by
SamGG • 170
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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 4 months ago by
SamGG • 170
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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`
...
written 5 months ago by
SamGG • 170
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... For an extensive example, take a look at the function cytof_addToFCS of cytofkit
...
written 5 months ago by
SamGG • 170
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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 6 months ago by
SamGG • 170
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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 7 months ago by
SamGG • 170
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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 8 months ago by
SamGG • 170
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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 8 months ago by
SamGG • 170
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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 9 months ago by
SamGG • 170
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