User: SamGG

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SamGG160
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160
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France
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3 weeks, 6 days ago
Joined:
4 years, 8 months ago
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Posts by SamGG

<prev • 55 results • page 1 of 6 • next >
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Comment: C: Queries related to limma package based analysis of masspectrometry data
... 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 SamGG160
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Comment: C: Newbie question: how do I address a subset obtained by split()?
... You have to store the result in a variable, then you can access it. res.split <- split(singlets, peaks) res.split$`area 2` ...
written 9 weeks ago by SamGG160
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Comment: C: Modifying or writing a FCS file in R using the FlowCore package
... For an extensive example, take a look at the function cytof_addToFCS of cytofkit ...
written 10 weeks ago by SamGG160
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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 SamGG160
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Comment: C: Load FlowCore to read .fcs files in R
... 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 SamGG160
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Comment: C: How to identify multiple datasets in FCS file through flowCore
... 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 SamGG160
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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 SamGG160
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Comment: C: How to identify multiple datasets in FCS file through flowCore
... 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 SamGG160
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Comment: C: Spillover matrix in FlowCore doesn't match Compensation Matrix from FlowJo
... 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 SamGG160
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Comment: C: Microarray expression analysis for on factor taking account confounders (covaria
... 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 SamGG160

Latest awards to SamGG

Popular Question 17 months ago, created a question with more than 1,000 views. For How to carry out a gene set analysis using custom gene sets?
Scholar 3.1 years ago, created an answer that has been accepted. For A: samr: understanding scoring line not parallel to diagonal; reproduce example C
Scholar 3.1 years ago, created an answer that has been accepted. For A: Problem with HDF5 and ncdfFlow

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