Let me bring you an external point of view. Reply to this email directly or view it on GitHub That the file is corrupt and should throw an error. It seems to me that's a pretty solid indicator
Question is, what should be the correct behaviour if BEGINDATA and the You guys use flowCore, so the file was presumably readable at some point? Keywords disagree on the start and end of the data segment. On 8:13 a.m., "Greg Finak" Does flowRespository modify theįCS file text segment at all? Came across an example where the header and Having said that, FlowJo does read this file, and so does Values is more likely to be correct, but this could be potentiallyĭangerous. You could implement some heuristics that would guess which of the two This applies to the Accuri - C6 - A02 Spherotech 8 Peak Beads.fcsįile. Match and that this needs to be manually fixed by the user before you can Reasonably sensible error message explaining that these two values do not
(this is NOT standard compliant, but unfortunately some vendors do putĩ9999999 in the HEADER instead of a large value that does not fit in there) If the HEADER says 99999999 then also use what's in the TEXT segment.If the HEADER says 0 then use what's in the TEXT segment (this is.If offset information in the FCS HEADER disagrees with what is in the Is 2da6c856cda1ed95a8aa01d8d5fb0de8, which matches the md5sum of the file Original file on our network drive and the md5sum Talking about Accuri - C6 - A02 Spherotech 8 Peak Beads.fcs, I dug out that And just to be really really sure, if you guys are Also, if you guys are talking aboutįR-FCM-ZZZ4, then this is a dataset that I have uploaded and I used theįiles as given to me by all the different vendors and I didn't use theĭe-identification feature since I wanted the files to stay exactly the way This never moves anything around in the file so all your (if the steam detects that the byte is inside a keyword value that shouldīe kept private). Each byte is either passed on, or replaced with a space character Upload client, and this intercepts the data as it is being sent to the Own DeIdentifyFCSInputStream (extends InputStream) as part of the data The only time FlowRespository modifies the header is whenĭe-identification is selected by the user.
May I know if this error occurs due to the fcs files or flowCore not installed properly or something else ? However, I was able to read the fourth file Accuri - C6.fcs Loaded via a namespace (and not attached): stats graphics grDevices utils datasets methods base Keyword: / is dropped because no value found!Ģ: In fcs_text_parse(txt, emptyValue = emptyValue) : The HEADER and the TEXT segment define different starting point to read the data.ġ: In fcs_text_parse(txt, emptyValue = emptyValue) : I tried to read them and they all got the following errorĮrror in readFCSdata(con, offsets, txt, transformation, which.lines, scale, : The dataset are the first 3 fcs files available in the Flow RepositoryĪccuri - C6 - A02 Spherotech 8 Peak Beads.fcs I was trying to use flowCore to read some fcs file from BD AccuriTM C6 Flow Cytometer.
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