scde.expression.difference outputs when batch defined

[ghost]

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?

[JEFworks]

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.works<http://jefworks.com/> On Mar 3, 2018, at 8:46 AM, Poorya Parvizi <[email protected]<mailto:[email protected]>> 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? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_hms-2Ddbmi_scde_issues_61&d=DwMCaQ&c=WO-RGvefibhHBZq3fL85hQ&r=2gb0vmLv11Vi98WTAqlCXyDkhi11d9lKeGWDXEU-qNw&m=8hTy00og004b00ERV41yIFVjg6M4Y64foUEmdmZMobI&s=Ef122AP__VQpifQ7LrzGmKw9TTGZ-K3wGpl3Ido-814&e=>, or mute the thread<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AIj2SBb1hm7X-5F6scI4WEO9OThwsC7gc3ks5tap60gaJpZM4Sa7HT&d=DwMCaQ&c=WO-RGvefibhHBZq3fL85hQ&r=2gb0vmLv11Vi98WTAqlCXyDkhi11d9lKeGWDXEU-qNw&m=8hTy00og004b00ERV41yIFVjg6M4Y64foUEmdmZMobI&s=Zl2tpAEQgGi6hHnjGRe46x6t6tQe0FXBirAN1KO79xE&e=>.