User: SamGG
SamGG • 190
- Reputation:
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- France
- Last seen:
- 4 days, 23 hours ago
- Joined:
- 5 years, 3 months ago
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Posts by SamGG
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... 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 5 days ago by
SamGG • 190
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... Hi,
2) the original code of FCSTrans is R code and could be found at https://sourceforge.net/projects/immportflock/files/FCSTrans/
Regards ...
written 5 days ago by
SamGG • 190
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... 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 22 days ago by
SamGG • 190
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... 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 weeks ago by
SamGG • 190
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... 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 weeks ago by
SamGG • 190
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... 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 weeks ago by
SamGG • 190
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... 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 10 weeks ago by
SamGG • 190
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... 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 10 weeks ago by
SamGG • 190
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... 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 10 weeks ago by
SamGG • 190
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... Thanks for your reply. Let us know about your feedback and if you could publish your code, it could be helpful for the community.
Best. ...
written 3 months ago by
SamGG • 190
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