Technical replicates for MaxQuant LFQ

[Claire Chew]

Hi, 

We are having trouble with dataProcess() for LFQ data generated from MaxQuant 

Essentially we have 3 conditions, 2 biological replicates and 3 technical replicates each, and each replicate has 2 fractions (total 12 raw files per condition). I have uploaded the annotation csv file here.

However, when we run dataProcess() we get this:

  Summary of Samples :

                           P18 P28 P35

# of MS runs                 1   1   1

# of Biological Replicates   2   2   2

# of Technical Replicates    0   0   0

 Summary of Missingness :

  # transitions are completely missing in at least one of the conditions : 15907

    -> DVYEDELVPVFEAVGR_2_NA_NA, GYELVPNLEIPTVNPVAIK_3_NA_NA, IPTAGIYGASYVPFAAPATATIATLQK_3_NA_NA, LFIGGIPK_2_NA_NA, TAEDSTAAM(Oxidation (M))SSDSAAGSSAK_2_NA_NA ...

  # run with 75% missing observations: NA

Error in if (sum(run.missing < 0.25) != 0) { : 

  missing value where TRUE/FALSE needed

How should we change our annotation file so it reflects the correct number of biological and technical replicates and we can perform the analysis? 

Thank you so much!

Claire

[Meena Choi]

Hi Claire,

I shortly review it. Here are some solutions for your case.

- Run column should be the same as Raw.file.

- if you have technical replicates, please add 'TechReplicate' column in annotation. I guess the current 'Run' column has tech replicate information. please replace the column name 'Run' to 'TechReplicate'

- If you have different subjects in each condition, please distinguish them in BioReplicate. For example, two bioreplicates in P18 are labeled 1 and 2, other two bioreplicates in P28 are labeled as 3 and 4, other two bioreplicates in P35 are labeled as 5 and 6.

Hope that it works.

- Meena

[Claire Chew]

Hi Meena, 

Thanks so much for your reply! 

Have edited the annotation file but am still getting this 

  Summary of Samples :

                           P18 P28 P35

# of MS runs                 6   6   6

# of Biological Replicates   2   2   2

# of Technical Replicates    2   2   2

For my experimental set up as described was expecting to see 

# of MS runs 6 

# of Biological replicates 2 

# of Technical replicates 3 

Is there anything I'm still missing?

Thanks so much!!

Sincerely, 

Claire 

[Claire Chew]

Apologies this is the annotation file