EVD: Top5 contaminants

[angelawu-wustl]

Hi,

I noticed that there are only 4 contaminants plotted for the Top5 contaminants, and I can't figure out why. I used the following to generate the report.

createReport(
txt_folder = "path to the txt folder",
yaml_obj = list()
)

Also, is the plot based on the proteinGroups.txt file or the evidence.txt file? In my case, one of the four contaminants' name is in the evidence.txt file, but not in proteinGroups.txt.

Please let me know if I should provide you the relevant .txt files.

Thank you, Angela

[cbielow]

hi,

if possible, please provide the .txt file. The name of the metric/plot usually indicates the underlying data, i.e. EVD: .. is evidence.txt, PG: ... is proteinGroups.txt etc...

cheers

[angelawu-wustl]

Hi,

Thank you for the response. Please see the attached for the evidence.txt file. evidence.txt

Best, Angela

[cbielow]

Hi,

problem 'solved':

The reason you are seeing only 3 contaminants is that some of the top5 contaminants have identical names, once you start shortening them for display purposes: Here

[1] "CON__P00761"                                                                           
[2] "Keratin, type II cuticular Hb2"                                                        
[3] "Transmembrane protease serine 13;Trypsin-1;Alpha-trypsin chain 1;Alpha-trypsin chain 2"
[4] "Keratin, type II cytoskeletal 1"                                                       
[5] "Keratin, type II cytoskeletal 8" 

These are the Top5, but three get shortened to Keratin, type.., which makes them collapse into one category (whose total intensity is correctly computed as the sum of the underlying proteins).

I hope this solves the confusion.

I've extended the help text to make everyone aware that this might happen.

[angelawu-wustl]

Hi,

Thank you for the explanation.

I have some other questions about PTXQC but not related to "issues", Is it better to send you email instead?

Thanks, Angela

[cbielow]

sure, see https://www.bsc.fu-berlin.de/About/index.html

[angelawu-wustl]

Thank you. I've sent an email to Dr. Chris Bielow. The email is coming from angela.wu@wustl.edu. Hope it didn't get sent to the spam folder.