User: SamGG

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SamGG90
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90
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France
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1 week, 3 days ago
Joined:
3 years, 10 months ago
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Posts by SamGG

<prev • 36 results • page 1 of 4 • next >
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Answer: A: How to select top 10% highly variable genes in microarray data?
... Hi, I am not an expert but IMHO your code is correct to achieve your goal. Selection should take place AFTER normalization, but if your samples are roughly similar there should be not much difference between after or before. Just a word concerning Z-score. It will relate the data to their dispers ...
written 10 days ago by SamGG90
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Comment: C: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array exte
... From a practical point of view, if I don't have an unstained sample, does using the use of a positive population and a negative population in each maker help at computing the spillover matrix? If so, do you know a piece code? ...
written 4 weeks ago by SamGG90
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Comment: C: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array exte
... Many thanks Mike! It could be helpful if you put this working example in the doc. Just a small remark. Although this example only illustrates the usage, the diagonal is not equal to 1. From what I understand, the current code divides the matrix values by the maximum of the rows, but not the values ...
written 4 weeks ago by SamGG90
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Comment: C: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array exte
... Thanks a lot for your explanation. Previously I played around with the FCS files from the compensation tutorial of FlowJo, but there is no unstained file if I understand correctly. Do you know a small dataset that includes all required files to try the spillover function ? ...
written 4 weeks ago by SamGG90
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Comment: C: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array exte
... I was not sure that you really want to compute the compensation matrix. I looked into the code but I didn't understand the rational behind. I found that interesting explanation at Roderer web that sounds easy although I doubt the background noise is taken into account (but may be there is no need). ...
written 4 weeks ago by SamGG90
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Comment: C: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array exte
... Here is the message I got once the set of FCS files are read > library(flowCore) > fs <- read.flowSet(files = dir(system.file("extdata", "compdata", "data", package="flowCore"), full.names=TRUE)) > spillover(fs, unstained = "NA", fsc = "FSC-Height", ssc = "SSC-Height", stain_match = "o ...
written 4 weeks ago by SamGG90
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Answer: A: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array exte
... Hi, I think the right way to read a set of FCS is the following. If I use your code, I get the same error. fs <- read.flowSet(files = dir(system.file("extdata", "compdata", "data", package="flowCore"), full.names=TRUE)) Moreover these example files do not seem to be use with the spillover func ...
written 4 weeks ago by SamGG90
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Answer: A: flowCore estimate logicle - error in getChannelMarker
... Hi, The code of the getChannelMarker function tries to find an exact match using of the .flowParamMatch function. By default the matching is not in fix mode (fix = FALSE) but considers the query as a regular expression. This leads to a call to the grepl() function. As the mentioned channel contains ...
written 6 weeks ago by SamGG90
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Comment: C: Please help me verify my compensation and spill matrices makes sense ( openCyto
... For sure, it sounds quite strange that the choice of fluorochromes leads to so many cross talk. I think the compensation using the spillover function might be tricky. Double check the fact "you'll need the single stained controls and the unstained control to calculate the spillover matrix with spill ...
written 3 months ago by SamGG90
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Answer: A: Please help me verify my compensation and spill matrices makes sense ( openCyto
... Based on the code available at https://github.com/RGLab/flowCore/blob/23d64cbb635ea7bb131b1047d2b97007b9813d93/R/flowFrame-accessors.R#L437, the compensation matrix is applied but does not seem to be assigned to the header of the FCS files. So what you observed makes sense to me. ...
written 3 months ago by SamGG90

Latest awards to SamGG

Scholar 2.3 years ago, created an answer that has been accepted. For A: samr: understanding scoring line not parallel to diagonal; reproduce example C
Scholar 2.3 years ago, created an answer that has been accepted. For A: Problem with HDF5 and ncdfFlow

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