JEFworks
commented
6 years ago Hi Poorya,
You can always find more information about these methods with ?scde.expression.difference
The data returned is a data frame with the following fields: \itemize{ \item{lb, mle, ub} {lower bound, maximum likelihood estimate, and upper bound of the 95% confidence interval for the expression fold change on log2 scale.} \item{ce} { conservative estimate of expression-fold change (equals to the min(abs(c(lb, ub))), or 0 if the CI crosses the 0} \item{Z} { uncorrected Z-score of expression difference} \item{cZ} {expression difference Z-score corrected for multiple hypothesis testing using Holm procedure} } If batch correction has been performed (\code{batch} has been supplied), analogous data frames are returned in slots \code{$batch.adjusted} for batch-corrected results, and \code{$batch.effect} for the differences explained by batch effects alone.
So you want the batch.adjusted list.
Jean Fan, PhD Bioinformatics and Integrative Genomics NCI F99/K00 Post-Doctoral Fellow Zhuang Lab | Harvard University 12 Oxford St, Naito 031, Cambridge, MA 02138 web: jef.workshttp://jefworks.com/
On Mar 3, 2018, at 8:46 AM, Poorya Parvizi notifications@github.com<mailto:notifications@github.com> wrote:
Hi Jean, I have a question that in scde.expression.difference when i use batch, the result gives three lists batch.adjusted, batch.effect and results. which one should i use to find significant in differential expression with batch effect elimination?
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Hi Jean, I have a question that in
scde.expression.differencewhen i use batch, the result gives three listsbatch.adjusted,batch.effectandresults. which one should i use to find significant in differential expression with batch effect elimination?