trouble with Msstats

[Pratyush Routray]

Hi, 

I am new to MSstats. While analyzing my data generated from FragPipe, I am encountering an error, even after generating a fraction column. 

I have two conditions, and each has three biological replicates. Each replicate was separated by SDS-PAGE into eight fractions. 

Error in .handleFractionsLF(input) :
  ** MSstats suspects that there are fractionations and potentially technical replicates too. Please add Fraction column to the input.

I would greatly appreciate any suggestions. I am using the current version of MSstats.

Thanks,

Pratyush

[Anthony Wu]

Hi Pratyush,

Would you be able to share a subset of your data (after generating a fraction column) where this is causing an issue?

Thanks,

Tony

[Pratyush Routray]

Hi Tony,

Thank you for looking into this.

Attached is a subset of my data that generates the issues in MSstats. When I used another set of my data, which is similar to this one, with only one biological replicate, I did not have any issues. 

Pratyush

[Anthony Wu]

Hey Pratyush,

I took your dataset and processed it through MSstats. I didn't encounter any issues (the only notable adjustment I made was turning off normalization, but that was because the subset of data you gave me only contained one fragment).   Could you confirm you've updated to the latest MSstats version 4.16.0?

Tony

[Anthony Wu]

Here's the code:

```

library(readxl)

library(MSstats)

input = read_excel("Data_Pratyush.xlsx")

msstats_format = FragPipetoMSstatsFormat(input = input)

quant = dataProcess(msstats_format, normalization = FALSE)

```