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]]

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]]