User: SamGG

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SamGG150
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Posts by SamGG

<prev • 51 results • page 1 of 6 • next >
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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 22 days ago by SamGG150
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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 7 weeks ago by SamGG150
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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 weeks ago by SamGG150
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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 8 weeks ago by SamGG150
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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 4 months ago by SamGG150
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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 4 months ago by SamGG150
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Comment: C: Microarray expression analysis for on factor taking account confounders (covaria
... Could you check the columns of the design by issuing colnames(design)? I am wondering whether "PHENO" is the correct way to name the column of interest. ...
written 4 months ago by SamGG150
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Answer: A: Exporting FCS from FlowJo for flowCore & cytofkit analysis
... Hi, I will give you quick answers, letting place for improvements by others more qualified than I am. 1. IIRC, linearize transform data linearly such that minimal value is zero and maximal is one. I always set transformation to FALSE. 2. If export is FCS v2, data are usually compensated and trans ...
written 4 months ago by SamGG150
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Answer: A: Microarray expression analysis for on factor taking account confounders (covaria
... Hi ! Short answer: you are trying to estimate nearly as many parameters as samples. The * in the formula means that you are looking for interactions between the factors as well as well the factors independently. In order to estimate the factors without interactions, replace * by +. Long answer: I gu ...
written 4 months ago by SamGG150
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Answer: A: Installation Problem: installation path not writeable, unable to update packages
... a) the final message might be simply a warning. If you do library(limma), do you get an error? If not, the limma package is correctly installed, but the others packages failed to be updated. Not a big deal if you installed R recently. b) if you want to install packages at another place, the simples ...
written 5 months ago by SamGG150

Latest awards to SamGG

Popular Question 13 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 2.8 years ago, created an answer that has been accepted. For A: samr: understanding scoring line not parallel to diagonal; reproduce example C
Scholar 2.8 years ago, created an answer that has been accepted. For A: Problem with HDF5 and ncdfFlow

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