User: alerodriguez

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Posts by alerodriguez

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Adjusting batch effects in microarray expression data using empirical Bayes methods
... Johnson and Li. 2007, Adjusting batch effects in microarray expression data using empirical Bayes methods, is the paper for the comBat package, and I have trouble understanding the following from page 119  ..... stabilize gene variances by shrinking variances across all other genes, possibly protec ...
microarray combat batch effects written 3 months ago by alerodriguez0 • updated 3 months ago by James W. MacDonald45k
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Comment: C: Removing batch effects with sva and combat using the sva package
... What is the output data format after applying comBat? More specifically, when applying linear models to remove batch effects one usually ends up with the residuals of the original data (expression data in my case). I would like to know what type of processing, normalization or transformations are do ...
written 3 months ago by alerodriguez0
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Comment: C: error when trying to apply the specific gene filter.
... Thanks for your answer, very helpful. Blessings.    ...
written 3 months ago by alerodriguez0
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Comment: C: error when trying to apply the specific gene filter.
... Thank you for your comment,something like this? f1 <- kOverA(0.50, 3.5) ffun <- filterfun(f1) flrGene <- genefilter(geneExpr, ffun) geneExpr<- geneExpr[flrGene, ]​   ...
written 3 months ago by alerodriguez0
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Answer: A: error when trying to apply the specific gene filter.
... f1 <- kOverA(0.50, 3.5) ffun <- filterfun(f1) flrGene <- genefilter(geneExpr, ffun) geneExpr<- geneExpr[flrGene, ]​ something like this? ...
written 3 months ago by alerodriguez0
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Data format after removing batch effects using linear model vs using comBat
... After removing batch effects using linear model the output data will be the residuals, what is the output form of the data when using ComBat? Residuals? Can you clarify, please? Thanks! ...
microarray sva combat residuals linear models written 3 months ago by alerodriguez0
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Answer: A: Agilent microarray chip normalization/background correction
... Regarding:a.) fit a batch effect in your linear model or b.) use ComBat() in the sva package to remove the batch effect.   After removing batch effects using linear model the output data will be the residuals, what is the output form of the data when using ComBat? Residuals? Can you clarify, please ...
written 3 months ago by alerodriguez0
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error when trying to apply the specific gene filter.
... Please help me understand why I get an error when trying to apply the specific gene filter. Please see details below: I am working with microarray data  dim()=54675    80 grouped by status table(gcrma.ExpressionSet$TG.binary) =group1=52 and group2=28 My data is in log2  #---------------------spe ...
genefilter written 4 months ago by alerodriguez0
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Comment: C: Non-specific filtering methodogies for ExpressionSet in R/Bioconductor
... I apologize, I'm very new to microarray data analysis would you please elaborate on the meaning of "mean log-expression".Thanks     ...
written 4 months ago by alerodriguez0
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removing batch effects using sva combat and linear regression
... After using comBat to remove know batch effects, I used sva to estimate unknown sources of variation. I saved the surrogate variables to my phenotype file and regress these variables along with other covariates as shown in the formula. x=lm(loc2[,i]~Age+Sex+surrogate.1+surrogate.2+batch, data=pData ...
combat sva microarry jeff leek written 4 months ago by alerodriguez0

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