Closed pejota66 closed 11 months ago
Hello,
It seems like one of your files has a very special encoding. Do you perhaps have any special characters in them?
Best, Sebastian
Hello,
thanks for your response. I am using the protein groups output from DIA-NN. the file name normally is similar to this: F:\K562_trial\Data\K562vsHELA_Swathand30SPD\HELA2.wiff
Is it acceptable?
Best, Pedro
Hello Pedro,
amica is not able to read .wiff files, these are raw files. Usually raw files come in strangely encoded and compressed formats, explaining the warning message.
For DIA-NN there should be a tsv file which filename usually ends with pg_matrix.tsv. The pg_matrix file contains the quantified protein groups, and should contain following columns for amica to be able to parse it:
https://github.com/tbaccata/amica/wiki/00-Accepted-input-formats#dia-nn
Best, Sebastian
Hello Sebastian,
There might have been a misunderstanding. The file used in AMICA is, of course, the pg_matrix.tsv from DIA-NN, not the WIFF file. However, you inquired if my table might contain any symbols, and I provided you with an example of a sample name from the protein groups table because the other things are the protein names and their abundance. Does this clarification make sense to you?
thanks, Pedro
Hey Pedro,
Ah I see, I misunderstood that.
After doing some digging, it is still a bit hard to tell what might went wrong...
Did you create your output using windows? Was there any post-processing in excel involved? After doing some digging the only explanation I can come up with, is that the file encoding might be a Windows UTF-16 encoding that R is struggling with reading in.
If you'd try to read in your pg_matrix in R using the read.delim
function do you get the same warning message?
Best, Sebastian
Hello,
when trying to upload DIA-NN output, this error pops up: "simpleWarning in readLines(inFile$datapath, n = 1): line 1 appears to contain an embedded nul"
How to fix it?
Thanks