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User: alison.sara.waller

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Posts by alison.sara.waller

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Error Combat (SVA)
... Hi there, I am analyzing high-throughput metabolomics data. The samples were run in 6 batches. I previously used sva/combat to normalize for the batch effects.  We have since re-run the feature finding, I am running my old script on new data and now getting an error.  The rows are the samples, an ...
sva written 13 months ago by alison.sara.waller0
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Comment: C: ComBat: Error non-conformable arguments
... Okay - oops I had a few extra entries in my  df$MSBa. Now I"m getting a different error re: non-conformable arguments > df_cmB<-ComBat(dat=t(as.matrix(df$dat)),batch=as.factor(df$MSBa),mod=NULL) Found 5 batches Found 0  categorical covariate(s) Standardizing Data across genes Error in ((dat ...
written 3.8 years ago by alison.sara.waller0
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Comment: C: ComBat: Error non-conformable arguments
... Thanks, I now have a new error.  And it thinks I have 10 batches when I only have 5. > df_cmB<-ComBat(dat=t(as.matrix(df$dat)),batch=df$MSBa,mod=NULL) Found 10 batches Found 0  categorical covariate(s) Standardizing Data across genes Fitting L/S model and finding priors Error in apply(s.data[ ...
written 3.8 years ago by alison.sara.waller0
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ComBat: Error non-conformable arguments
... Dear all, I have a large metabolomics data set. About 6000 samples were run over a few months in 5 batches, or 61 batches (depending on definition). At the moment for each sample I have the intensity for 21 peaks (metabolites).     > head(df$dat)                                           peak1 ...
combat written 3.8 years ago by alison.sara.waller0 • updated 3.8 years ago by James W. MacDonald49k
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Comment: C: rownames for categoryReshape
... Thanks, this is great, and much faster than the categoryReshape function in plotrix. And incase anyone was wondering, by comparing the results I can see that the column names from categoryReshape, are in the order of sort(unique(df$Gene)). ...
written 4.2 years ago by alison.sara.waller0
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rownames for categoryReshape
... Dear All, I am trying to make incidence matrices (where each row represents a pathway, and each column a gene) and there is a 1 if that gene is in the pathways, otherwise it is a zero. I am using the function categoryReshape from the package plotrix as follows: df_incid<-t(categoryReshape(df)) ...
category written 4.2 years ago by alison.sara.waller0 • updated 4.2 years ago by Martin Morgan ♦♦ 22k

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Popular Question 3.8 years ago, created a question with more than 1,000 views. For ComBat: Error non-conformable arguments

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