Error in quantile.default(med_cor, p = 0.25)--missing values and NaNs not allowed...

[DanSchnell]

Hi,

I installed batchQC from BIoconductor (today) and ran 2 of the examples--worked very well.

I'm trying with my own data, and got this error (before GUI activated):
Quitting from lines 178-179 (batchqc_report.Rmd)
Error in quantile.default(med_cor, p = 0.25) :
missing values and NaN's not allowed if 'na.rm' is FALSE

No NAs or NaNs in the expression data, batch or condition objects...
condition & batch vectors are type character.
Expression data has 189 samples & ~ 16K features (features z-scored)

table(condition,batch,useNA='always')
batch
condition 2014 2016 2017 2018 2020
25minus 5 1 7 9 6 0
26_31 0 4 8 4 1 0
32_37 6 1 17 54 22 0
38plus 5 1 10 19 9 0
0 0 0 0 0 0

Any thoughts on getting past this error?

Thanks much!

[mani2012]

You can try changing some of the 1 below to 0 in the report_option_binary option for troubleshooting purpose: report_option_binary="111111111" to report_option_binary="110111111" But you may have to see whether you are passing the data correctly or for other issues in data. From: DanSchnell ***@***.***> Sent: Thursday, June 10, 2021 2:07 PM To: mani2012/BatchQC ***@***.***> Cc: Subscribed ***@***.***> Subject: [mani2012/BatchQC] Error in quantile.default(med_cor, p = 0.25)--missing values and NaNs not allowed... (#21) Hi, I installed batchQC from BIoconductor (today) and ran 2 of the examples--worked very well. I'm trying with my own data, and got this error (before GUI activated): Quitting from lines 178-179 (batchqc_report.Rmd) Error in quantile.default(med_cor, p = 0.25) : missing values and NaN's not allowed if 'na.rm' is FALSE No NAs or NaNs in the expression data, batch or condition objects... condition & batch vectors are type character. Expression data has 189 samples & ~ 16K features (features z-scored) table(condition,batch,useNA='always') batch condition 2014 2016 2017 2018 2020 25minus 5 1 7 9 6 0 26_31 0 4 8 4 1 0 32_37 6 1 17 54 22 0 38plus 5 1 10 19 9 0 0 0 0 0 0 0 Any thoughts on getting past this error? Thanks much! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#21>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACMB4PHPFIDHHVRKVC6KSLLTSD5NJANCNFSM46PAQWCQ>.

[DanSchnell]

Thanks for getting back to me.

I seem to have resolved the issue by adding a a positive constant (100) to each entry of the expression matrix--suspecting that the code was not expecting negative numbers or all feature means==0.

Best,
Dan