Error with dataProcess

[xyztlmercury]

Hi,

I recently updated my R and MSstats since I cannot use the old version anymore.

I used my script for earlier version of MSstats and got the error message below: quant.skyline <- dataProcess(raw = input.skyline,

• logTrans=2,
• normalization = 'globalStandards', ##changed to global standard
• nameStandards = 'sp|Q9H6Q4|CIAO3_HUMAN',
• summaryMethod = 'TMP',
• MBimpute=TRUE,
• censoredInt='0', ## important for Skyline
• cutoffCensored='minFeature',
• maxQuantileforCensored = 0.999) Error in dataProcess(raw = input.skyline, logTrans = 2, normalization = "globalStandards", : unused argument (cutoffCensored = "minFeature")

I then removed the unused argument but still got an error: quant.skyline <- dataProcess(raw = input.skyline,

• logTrans=2,
• normalization = 'globalStandards', ##changed to global standard
• nameStandards = 'sp|Q9H6Q4|CIAO3_HUMAN',
• summaryMethod = 'TMP',
• MBimpute=TRUE,
• censoredInt='0', ## important for Skyline

• cutoffCensored='minFeature',

• maxQuantileforCensored = 0.999) Error in if (cutoff_lower <= 0 & !is.null(missing_symbol) & missing_symbol == : missing value where TRUE/FALSE needed

I am wondering if you could help me with it.

Thank you.

[mstaniak]

Can you share a small data example that reproduces this issue?

[xyztlmercury]

Dear Mateusz,

Thank you very much for your reply.

I have attached the MSstats input file, annotation file as well as the R script that produces this issue.

Please don't hesitate to let me know if you need additional information from my side.

Thank you and I am looking forward to your reply.

Sincerely, Xiaorui

On Wed, Apr 27, 2022 at 5:48 AM Mateusz Staniak @.***> wrote:

Can you share a small data example that reproduces this issue?

— Reply to this email directly, view it on GitHub https://github.com/Vitek-Lab/MSstats/issues/87#issuecomment-1110959410, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGHL4PIJQ3PFI2ON526FE6LVHEZRJANCNFSM5UHA6CLQ . You are receiving this because you authored the thread.Message ID: @.***>

[mstaniak]

Hi, I can't see the attachments, please try sending them directly via e-mail or adding them via Github comment

[xyztlmercury]

Hi Mateusz,

I replied this email directly last time. I am wondering if there is another email address that I could use?

Thank you and I'm looking forward to your reply.

Sincerely, Xiaorui

On Thu, Apr 28, 2022 at 4:18 AM Mateusz Staniak @.***> wrote:

Hi, I can't see the attachments, please try sending them directly via e-mail or adding them via Github comment

— Reply to this email directly, view it on GitHub https://github.com/Vitek-Lab/MSstats/issues/87#issuecomment-1112083248, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGHL4PJ7MFFWMLNXNRFX3X3VHJXZDANCNFSM5UHA6CLQ . You are receiving this because you authored the thread.Message ID: @.***>

[mstaniak]

Hi, please use the e-mail address indicated in the DESCRIPTION file of the package