search for: cytometry

Hi all. How do I extract date from fcs format file with R. I.e I'd like make statistical analysis using R-program, but I don't know if there are R-packets for fcs format file, and using examples. Thanks. Pta: In Linux SO exist any program that transform from fcs format to ASCII text file?

Hi all. I'd like know what is the format file saved by Leica Microsystems TCS SP2-AOBS equipped with a SP2-FCS2 Leica Microsystems workstation its datas. Cause it save in *.fcs extention file but ins't flow cytometry standart format file... Tahnks Horacio.

Hi there, I use function "kmeans" and "clara" to cluster one flow cytometry dataset. By using function "plot", the clusters got from "clara" can be graphed, while "kmeans" not. How can I get the plot of the clusters of "kmeans"? And, I hope to compare the two methods "kmeans" and "clara", or in other word, I w...

...mounts of DNA. I am interested in knowing how much of the cell populations are in each peak as well as between. I am not really sure how to go about it; I have been considering fitting a gaussian distribution to each peak and integrate the part between the peaks as described by Watson et al (1987 Cytometry 8:1-8). A more straight forward and more visual approach appears to be plotting the cumulative frequencies. In either case, I should like to find the peaks in the histogram automatically, as well as getting proper information about the peaks. How would I go about finding peaks using R? Also I have...

...;> jpeg("test.jpeg", bg="orangered") >> plot(1:10, 1:10, col="green") >> dev.off() >There was a Windows-specific bug, for which I've just committed a fix How can I display a bmp directly in R? When plotting 100,000+ points (common with flow cytometry data) [or even the 10,000s of points with microarray data] the Windows metafile is not the way to go (nor is postscript) because the files are too large and repainting them takes too long. Does R provide a way to plot to a bmp and then display that graphic immediately? It's a pain to leave R...

Hi there, I'm trying clustering methods on flow cytometry data. We want to evaluate the clustering results and compare the validation methods. So far the cluster validation functions I found in R are: cluster.stats{fpc} cl_agreement{clue} Are there other validation functions in R? Thank you! [[alternative HTML version deleted]]

...required is enormous. There is at least one exception to this. Single-linkage hierarchical clustering with a convex distance such as Euclidean distance is feasible for quite large data sets using algorithms for the Euclidean minimum spanning tree. For tens to hundreds of thousands of points (flow cytometry data) the algorithm in the nnclust package is competitive in speed with model-based clustering (on a 32-bit system). It's slower than pam(), but it is deterministic. This doesn't apply to the original question, of course. -thomas

Hello I have been trying to get WinMDI (a program for reading flow cytometry data in windows) working under wine. WinMDI has an appdb entry of http://appdb.winehq.org/appview.php?appId=2850 . I had the early versions of this program working under wine 20050930 and 20050725. I recently upgraded from 20050930 to 0.9.7 on my FreeBSD 6.0 box, and tried to run the same ver...

Hellos, I am looking for a package that can scrub values from flow cytometry data file keywords that have either the "$" or "@" keyword prefix. Are their any options out there? The options from WEHI, TreeStar, and whoever made "File Sanitizer" aren't working. thanks for any help on this, -- - suzanne -----------------------------------...

...Research UK Manchester Institute is a centre for excellence in cancer research. We occupy state-of-the-art laboratories and provide exceptional core facilities including next generation sequencing, mass-spectrometry, advanced imaging, High Performance Computing, bioinformatics, histology, and flow cytometry. We are core-funded by Cancer Research UK (www.cancerresearchuk.org), the world?s largest cancer organisation, are an Institute of The University of Manchester (www.manchester.ac.uk), and are adjacent to The Christie NHS Foundation Trust (www.christie.nhs.uk), one of the largest cancer treatment ce...

...ce, or internship and/or coop ; or a Master's degree with a minimum of 6 years relevant work experience. Required: - Experience with machine learning methods applied to analysis of very large data generated by high-throughput life science technology such as, for example, NGS, Proteomics, Flow Cytometry, Imaging, or High-Throughput screening. - Excellent computer skills. Advanced R-programming experience. Knowledge of C, C++, Python, Matlab, SAS in Windows and Unix/Lunix environment. - Strong interest in statistical research and application of novel methods demonstrated by publication record -...

Hello list! I would like to fit a distribution to each of the peaks in a histogram, such as this: http://photos1.blogger.com/blogger/7029/2724/1600/DU145-Bax3-Bcl-xL.png . The peaks are identified using Petr Pikal peaks function ( http://finzi.psych.upenn.edu/R/Rhelp02a/archive/33097.html), but after that I am quite stuck. Any idea as to how I can: Fit a distribution to each peak Integrate the

Hello all, I am using the clustering functions in R in order to work with large masses of binary time series data, however the clustering functions do not seem able to fit this size of practical problem. Library 'hclust' is good (though it may be sub par for this size of problem, thus doubly poor for this application) in that I do not want to make assumptions about the number of