search

nolanlab / spade

SPADE: Spanning Tree Progression of Density Normalized Events
Other
48 stars 23 forks source link

Error during SPADE run #28

Closed krovi137 closed 12 years ago

krovi137 commented 12 years ago

Hi guys,

I'm new to both R and Cytoscape. I was actually attempting to do analysis on a data set which was not generated by flow cytometry. I figured that it wouldn't matter since the values were numerical in nature. I converted my csv files to fcs files and then attempted to analyze them using SPADE. I got all the way to the Run SPADE option and then was hit with the following error in the execution console:

Loading required package: igraph Loading required package: methods Scalable Robust Estimators with High Breakdown Point (version 1.3-01) Warning message: replacing previous import '.Ccharacter' when loading 'methods' Downsampling file: ./JB1~1.fcs Error in readFCSdata(con, offsets, txt, transformation, which.lines, scale, : Don't know how to deal with $BYTEORD 1234 Calls: SPADE.driver ... SPADE.addDensityToFCS -> SPADE.read.FCS -> read.FCS -> readFCSdata Execution halted

I'm not quite sure what that means. Have you guys encountered it before? Is it easy to handle and if so, what can I do to resolve it? And if it helps, I am using a PC.

Please let me know if you can assist me in any fashion. Thanks a lot. Harsha

krovi137 commented 12 years ago

oh and JB1~1.fcs is the name of the fcs file that I generated using my csv file.

zbjornson commented 12 years ago

Hello Harsha!

The digits of $BYTEORD in the header need to be separated by commas, e.g. "1,2,3,4", to meet the FCS file specification. Try changing that and please let us know how this works for you.

Best, Zach