error in uploading data from DIA-NN

[pejota66]

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

[tbaccata]

Hello,

It seems like one of your files has a very special encoding.
Do you perhaps have any special characters in them?

Best,
Sebastian

[pejota66]

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

[tbaccata]

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

[pejota66]

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

[tbaccata]

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