Jeannine- I have been working on research databases for flow cytometry for the last couple of years and would suggest using CellQuest's export feature rather than hand entering your values. I personally prefer FlowJo's analysis and export features, but under CellQuest's File menu you will find a function "Export" that will export all of the statistics in your file into a tabbed text file that can be opened in Excel. I believe there is also a checkbox for having data appended to an existing file. If I remember correctly, there is also a batch processing function, such that you could have a template for analysis run through your samples and perform this export automatically as each new file is analyzed. The problem that I saw with CellQuest was a difficulty with labelling a particular row of data with something meaningful. As far as I can tell from looking back at an export we did a couple of months ago, each separate row of statistics data that you see in a CellQuest analysis, i.e. UL,UR,LL,or LR from quadrant analyses or M1, M2 statistics from histograms, will be exported as one row into the spreadsheet file with all of the associated header information attached to the beginning of the row. The old CellQuest export file that I'm looking at has in one row all of the following information: File Name/Sample ID/Patient ID/Patient Name/Case Number/Acquisition Date/Gate/Gated Events/Total Events/Label/% Gated/% Total/X Mean/X Geo Mean/Y Mean/Median such that you have in just one row all of the last six parameters as data values pertaining to the one "Label" (UL,UR,LL,LR,M1,M2...). but also no columns that describe the stains that were used. In our analysis file, we had seven sets of stains and while working with CellQuest, the only thing that I tried was exporting the whole report that the clinical flow lab had provided to us. In retrospect, I would probably make a new analysis template for each set of stains (i.e CD3/CD19/CD8/CD4 or CD45RA/CD62L/CD8/CD4), and export the data into separate stain specific files. In the assumed absence of having CellQuest export a meaningful label for something like a quadrant statistic or a histogram marker, this approach could facilitate relabelling the data with something useful(i.e. a row of data from a dotplot of CD3/CD19 should be labelled as either "CD3+CD19-" or "T cells" rather than just the "LR" that CellQuest uses). You might also narrow the analysis even further and make an analysis template that just exports one dotplot's quadrant analysis or a histogram's statistics so that you can go back in Excel and do a find and replace in the label column; "T cells" for "LR", "B cells" for "UL"... You might need a lot of separate analysis templates, but then could recombine the data into one file after a little post-analysis processing. There's always more than one way to get the job done...try the export on a file, turn off some of the parameters that are exported, redo the export, and compare the resulting files. Playing around like this might give you a better idea of what labels, i.e. File, Patient Name,Gate, you really need for each row that is exported. Feel free to e-mail if you need more detailed information. Hope this helps! Todd At 05:18 PM 6/6/2002 -0400, you wrote: >Hello to all the helpful, and far-more-knowledgable-than-me flow >cytometrists out there: > >I've been involved in what started out as a relatively small >cytometry-based human study that has recently ballooned into something >much larger (10-fold increase in study participants, and still >growing). I have been taking my flow data, hand-entering it into >spreadsheet databases, which get sent to a statistician to correlate >with other clincal features of the diseases we are studying. What >started out as a relatively simple task (typing flow values into an >Excell database) has become more and more time-consuming. My question >is for those of you especially who run clinical flow cytometry labs that >generate high volumes of data: How do you manage the data once it is >generated? Are there any programs available that take the data >automatically once the samples have been run and enter the values >directly into a spreadsheet? Or do you hire work study students to do >this for you?? Please help me! > >I'm running a FACSCalibur, and CellQuest software. > >Thanks a bunch! > >Jeannine Navratil >University of Pittsburgh Todd A. Johnson Computer Systems Manager UCSD, Department of Psychiatry Dimsdale Lab CTFA 309/ MC 0804 (619) 543-2504 tajohnson@ucsd.edu
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