Question: spillover method in flowCore package
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gravatar for Frederico Arnoldi
9.0 years ago by
Frederico Arnoldi40 wrote:
Dear list, I am having problems with the "spillover" method of the flowCore package. I am trying to compensate a flowset but everytime I tried to get the spillover matrix from my control data, I received the following error message: "Error in .local(x, ...) : subscript out of bounds" In my flowset I have 6 flowframes (in the following order: unstained cells, APC, PercPCy5.5, FITC, PeCy7, PE) that I have loaded as following: >library("flowCore") >library("flowViz") >fs = read.flowSet(path = "path") >fs A flowSet with 6 experiments. column names: FSC-H SSC-A FITC-A PE-A PerCP-A PE Cy7-A APC-A Time I tried to get the spillover matrix with > comp.mat <- spillover(fs, unstained=1, fsc = "FSC-H", ssc= "SSC-A") Error in .local(x, ...) : subscript out of bounds I can not identify where is my mistake. I tried a fast look in the source code of "spillover method" (starting at line 525 of the flowSet-accessors.R in the flowCore_1.8.3.tar.gz), but I also not able to identify the source of my error or a possible bug. Please, could anyone help me with it? Thanks in advance, Fred _________________________________________________________________ Com o Internet Explorer 8 você fica mais protegido contra ameaças da web. Saiba mais. [[alternative HTML version deleted]]
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ADD COMMENTlink modified 9.0 years ago by Nishant Gopalakrishnan340 • written 9.0 years ago by Frederico Arnoldi40
Answer: spillover method in flowCore package
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gravatar for Nishant Gopalakrishnan
9.0 years ago by
Nishant Gopalakrishnan340 wrote:
Hi Frederico, Your flowSet appears to have 1 unstained sample and 5 single stained controls for APC, PercPCy5.5, FITC, PeCy7 and PE . The column names of fs have FITC-A, PE-A, PerCP-A, PE, Cy7-A and APC-A ( 6 channels). Can you try to call spillover after removing the columns corresponding to Time and the missing channel for which you do not have single stained samples for from the flowSet ? Nishant On 03/26/2010 08:01 AM, Frederico Arnoldi wrote: > Dear list, > > I am having problems with the "spillover" method of the flowCore package. I am trying to compensate a flowset but everytime I tried to get the spillover matrix from my control data, I received the following error message: > > "Error in .local(x, ...) : subscript out of bounds" > > In my flowset I have 6 flowframes (in the following order: unstained cells, APC, PercPCy5.5, FITC, PeCy7, PE) that I have loaded as following: > > >> library("flowCore") >> library("flowViz") >> fs = read.flowSet(path = "path") >> fs >> > A flowSet with 6 experiments. > > column names: > FSC-H SSC-A FITC-A PE-A PerCP-A PE Cy7-A APC-A Time > > > I tried to get the spillover matrix with > > >> comp.mat <- spillover(fs, unstained=1, fsc = "FSC-H", ssc= "SSC-A") >> > Error in .local(x, ...) : subscript out of bounds > > I can not identify where is my mistake. I tried a fast look in the source code of "spillover method" (starting at line 525 of the flowSet-accessors.R in the flowCore_1.8.3.tar.gz), but I also not able to identify the source of my error or a possible bug. > > Please, could anyone help me with it? > > Thanks in advance, > Fred > _________________________________________________________________ > Com o Internet Explorer 8 você fica mais protegido contra ameaças da web. Saiba mais. > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD COMMENTlink written 9.0 years ago by Nishant Gopalakrishnan340
Dear Nishant, Thanks for helping me! And sorry for sending the email in HTML for the list. > Your flowSet? appears to have 1 unstained sample and 5 single stained controls for? APC, PercPCy5.5, FITC, PeCy7 and PE . The column names of fs have> > FITC-A, PE-A, PerCP-A, PE, Cy7-A and APC-A ( 6 channels). > >Can you try to call spillover after removing? the columns corresponding to Time and the missing channel for which you do not have single stained samples > for from the flowSet ? In fact, I just have 5 stained channels. I my previous email "PE Cy7-A"? looked like two dyes instead of one. > colnames(fs) [1] "FSC-H"??? "SSC-A"??? "FITC-A"?? "PE-A"???? "PerCP-A"? "PE Cy7-A" "APC-A"?? [8] "Time" When I use the following command, the Time column is eliminated, as we can see in the output. > fs[,1:7] A flowSet with 6 experiments. ? column names: ? FSC-H SSC-A FITC-A PE-A PerCP-A PE Cy7-A APC-A However, when I use it in the spillover method, I still having the same error. > comp.mat <- spillover(fs[,1:7], unstained=1, fsc = "FSC-H", ssc= "SSC-A") Error in .local(x, ...) : subscript out of bounds Thanks again, Fred _________________________________________________________________ N?o deixe rastros ao navegar na Internet. Instale Gr?tis o Internet Explorer 8 agora.
ADD REPLYlink written 9.0 years ago by Frederico Arnoldi40
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