User: SamGG

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SamGG190
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190
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France
Last seen:
2 months ago
Joined:
5 years, 7 months ago
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s***************@inserm.fr

Posts by SamGG

<prev • 74 results • page 1 of 8 • next >
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Comment: C: Question regarding model matrix in limma.
... reprex is a convenient way to share code that is self sufficient aka reproducible. https://cran.r-project.org/web/packages/reprex/index.html Best. ...
written 3 months ago by SamGG190
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Comment: C: FCSTransTransform() implementation in flowCore
... The `estimateLogicle` function usually does a good job. Look for it in [HowTo-flowCore][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/flowCore/inst/doc/HowTo-flowCore.pdf ...
written 3 months ago by SamGG190
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Comment: C: FCSTransTransform() implementation in flowCore
... Hi, 2) the original code of FCSTrans is R code and could be found at https://sourceforge.net/projects/immportflock/files/FCSTrans/ Regards ...
written 4 months ago by SamGG190
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Comment: C: Sanity Checking Mixed Factorial Proteomics Analysis Workflow Using Limma
... Concerning the part before limma.I don't know from which instrument your proteomics data came out. Usually, a log transform is needed. It's not clear if it's already applied. You should also check graphically the VSN and the impute steps by plotting the replicates (or the samples) before and after e ...
written 4 months ago by SamGG190
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Comment: C: polyFunctions gate in OpenCyto 1.20
... Well I don't see the problem.The CSV will help the openCyto team. I would recommend you to check 2 lines starting with quotes. I am not sure whether it's OK to put comma and space in the alias. May be you can try without those lines. HTH "CD4+CD45RA-CCR7+, CD4+CD45RA+CCR7+ , CD4+CD45RA+CCR7- ...
written 4 months ago by SamGG190
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Comment: C: polyFunctions gate in OpenCyto 1.20
... Hi, Could you upload the CSV file? The link points to the Excel file and there could be some hidden post-processing. From the warnings, it looks like the ":" was replaced by "&", which is not recognized. HTH ...
written 4 months ago by SamGG190
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Comment: C: flowCore install missing a dependency?
... Hi, It seems that robustbase is not needed by flowCore. https://bioconductor.org/packages/release/bioc/html/flowCore.html FlowCore depends on rrcov which depends on robustbase. https://cran.r-project.org/web/packages/rrcov/index.html Please report if rrcov is installed or not on your session. To ...
written 4 months ago by SamGG190
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Comment: C: Help with Limma F.p.value from eBayes
... Thanks for your reply and pointing the interesting post you wrote more than ten years ago (you are a library definitively). As answered also to Aaron, could you point me any **peer reviewed article** that discuss the benefits of carrying out t tests directly over the F-then-t strategy in the contex ...
written 6 months ago by SamGG190
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Comment: C: Help with Limma F.p.value from eBayes
... Thanks for your reply. In my case, the "F-test before t-test" strategy comes from the ANOVA. Could you point me any **peer reviewed article** that discuss the benefits of carrying out t tests directly over the F-then-t strategy in the context of high-dimensional data? Or is it a property of the lin ...
written 6 months ago by SamGG190
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Comment: C: Help with Limma F.p.value from eBayes
... Dear Aaron, May I ask you to comment the two following simulations based on your simulation concerning F vs t test. Here I increased the number of replicates from 2 to 4 and set the number of DE genes to 300. I don't feel any interest in estimating an effect with two samples. In that case, F is fin ...
written 6 months ago by SamGG190

Latest awards to SamGG

Popular Question 9 months ago, created a question with more than 1,000 views. For How to carry out a gene set analysis using custom gene sets?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How to carry out a gene set analysis using custom gene sets?
Scholar 4.0 years ago, created an answer that has been accepted. For A: samr: understanding scoring line not parallel to diagonal; reproduce example C
Scholar 4.0 years ago, created an answer that has been accepted. For A: Problem with HDF5 and ncdfFlow

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