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syspremed / exploBATCH_serial

Explore batch effect (exploBATCH) is a package for discovering and correcting for batch effect using an approach in Nyamundanda et al (2017)
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No SDselect option in expBatch Function #1

Open chungtseng opened 6 years ago

chungtseng commented 6 years ago
  1. How to change the limit for the number of spectral bins? It seems that if the number of spectral bins is more than 375, it will cause error.
  2. Also for the vignettes, the plots are not showing
smanne07 commented 6 years ago

Hi,

Is there any update on fixing the error

"Spectral dimension is too large for current computation capabilities. Reduce the number of spectral bins to less than 375"

How do we change it?

Thank you

syspremed commented 6 years ago

Hi.

Sorry for late reply. This issue is associated with the old version of exploBATCH in which the number of features is limited to 375 only. So you can reduce the number of features by selecting the most variable features before applying the tool.

However, we have another version of exploBATCH (called exploBATCH_serial) in which the number of features are NOT limited BUT depending on the number of samples the tool can be slow for more than 1500 features (see runtime profiles in supplementary Figure 5 of the our paper "A Novel Statistical Method to Diagnose, Quantify and Correct Batch Effects in Genomic Studies.") . We have added an argument SDselect to allow the use to filter the number of features based on the variability of the feature. You can also find this new version exploBATCH on our github account (syspremed/exploBATCH_serial)

Thanks,

Gift.