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mani2012 / BatchQC

Provides Quality Control of sequencing samples by deducing if there is batch effect and adjusts for it.
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Error in quantile.default(med_cor, p = 0.25)--missing values and NaNs not allowed... #21

Open DanSchnell opened 3 years ago

DanSchnell commented 3 years ago

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 commented 3 years ago

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!

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DanSchnell commented 3 years ago

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