spectraCounteBayes Warning messages

[NaixiangYu]

Hello, I have tried to analyse my label-free data by referring to the tutorial "DEqMS analysis using MaxQuant outputs (label-free data)", but when I run the code fit4 = spectraCounteBayes(fit3), R pops up a warning message. How can I fix it?

Thanks,
Nai xiang Yu

[yafeng]

@yudada2020 Hi, please check the input expression matrix if there are proteins with missing values.
DEqMS requires at least two values for each group.

Yafeng

[NaixiangYu]

Hello, Dr yafeng, I have used the code "df.LFQ.filter = df.LFQ[df.LFQ$na_count_H<2 & df.LFQ$na_count_L<2,1:34]" as per your suggestion to perform missing value removal for the protein expression matrix but the same error is reported. Interesting to be able to output seemingly normal results. Attached is my input protein expression matrix.

Thanks,
Naixiang

test_LFQ.intensity.txt

[longchung90]

Hi Yafeng, it is such a wonderful script, thanks for sharing with us.

I did encounter a problem when I run fit4 = spectraCounteBayes(fit3)

The error came out as
Error in model.frame.default(formula = logVAR ~ x) : variable lengths differ in DeqMS (found for 'x')

Do you have any ides?

Thank you very much in advance!
L

[yafeng]

@yudada2020 Hi, i checked your input data frame, you should use
df.LFQ.filter = df.LFQ[df.LFQ$na_count_H<2 & df.LFQ$na_count_L<2,c(1,4:37)] (don't keep column 2, 3 )
and don't forget to do log2 transformation.
protein.matrix = log2(as.matrix(df.LFQ.filter))

if you still encounter error, check the peptide count table, it should contains peptide count per protein.

Yafeng

[yafeng]

@longchung90
Hi, i suspect there are missing values in fit3$count, which stores the peptide count per protein.
Try min(fit3$count) to see if all proteins have valid peptide count. If it returns NA, then one of your proteins contains NA for peptide count.

Yafeng

[yafeng]

@longchung90
Hi, i suspect there are missing values in fit3$count, which stores the peptide count per protein.
Try min(fit3$count) to see if all proteins have valid peptide count. If it returns NA, then one of your proteins contains NA for peptide count.

Yafeng

[longchung90]

Hi Yafeng,
I've run the script it got back to me this:

min(fit3$count)
[1] Inf
Warning message:
In min(fit3$count) : no non-missing arguments to min; returning Inf

Sorry I am not very experienced, I just started doing some bioinformatics. Thank you

[yafeng]

That’s the reason. fit3$count should be the PSM or peptide count for the protein. Inf or NA or negative number is not allowed. You need to check your input and command where the Inf value come from. Yafeng 在 2024年8月7日，12:06，Long Chung ***@***.***> 写道：  Hi Yafeng, I've run the script it got back to me this: min(fit3$count) [1] Inf Warning message: In min(fit3$count) : no non-missing arguments to min; returning Inf Sorry I am not very experienced, I just started doing some bioinformatics. Thank you — Reply to this email directly, view it on GitHub<#14 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAXG6N5JPAG7U3QY4TG6PPLZQGMKRAVCNFSM6AAAAABE5SX3JSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZSGU3TEOJZGE>. You are receiving this because you commented.Message ID: ***@***.***>