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bioinfoUGR / sRNAtoolbox

small RNA analysis programs: standalone jar files (sRNAbench, sRNAde, etc), manuals and Docker image
MIT License
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how to correct for batch effect #8

Open amarinderthind opened 1 year ago

amarinderthind commented 1 year ago

I am wondering if there is any option to adjust for batch correction and where to find the raw count file.

sert23 commented 1 year ago

since the matrix generation button is currently down, you can also generate a matrix count by launching a sRNAde job with all the samples that interest you.

Regarding batch effect correction, sRNAtoolbox does not provide this option but feel free to combine with approaches developed by other authors (e.g. https://academic.oup.com/nargab/article/2/3/lqaa078/5909519)

amarinderthind commented 1 year ago

@sert23 Thank you for getting back to me, I tried sRNAde and in the output, I just got the normalized count, not the raw count. For combat+deseq2 or RUV approach I need a raw count file. Do I miss something in the output, Could you please guide where I can find it? If not available through sRNAde, I will also be happy to merge data from individual samples to make the matrix, it would be great if you can guide me on the actual raw count at this level.

sert23 commented 1 year ago

if you download the whole zipped folder with the results, you will find it in: ./de/ttest/mature_sense_minExpr1_RCadj.mat Hope that helps

amarinderthind commented 1 year ago

Thank you @cris12gm , it was helpful. sorry for the late reply.