pcaMethods
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hredestig
Perform PCA on data with missing values in R
Hello @hredestig, I'm a [Sweave2Rmd](https://github.com/Bioconductor/sweave2rmd) volunteer. @jwokaty and I are trying to replace Bioconductor Sweave vignettes with R Markdown. It has many advantages over Sweave vignettes, such as R Markdown...
Hello! I ran upon a strange behavior of the DModX() function when projecting new data into my PCA model. I've pasted some code to reproduce this below. First, I train...
``` * checking R code for possible problems ... NOTE BPCA_initmodel: no visible global function definition for ‘cov’ Q2: no visible global function definition for ‘txtProgressBar’ Q2: no visible global...
Running, on [this dataset](https://github.com/hredestig/pcaMethods/files/10579068/norm.tsv.txt), these commands ``` library("pcaMethods") df
I'm trying to calculate the RMSE to do dimensionality selection but the model only gives me the matrix with data imputed. Is there any way to get the inverse transformed...
Hey there! I am trying to run ```llsImpute``` on my [spectracounts](https://github.com/hredestig/pcaMethods/files/9764891/spectracounts.tsv.txt), with the following commands: ``` library("vsn") library("pcaMethods") pdata = as.matrix(read.table('spectracounts.tsv.txt', sep='\t', h=T, row.names=1)) pdata[pdata==0] = NA norm = justvsn(ExpressionSet(pdata))...
Dear pcaMethods team, While teaching a class last week we have realized that `slplot` will fail if called from inside a function with the error: ```R Error in plot.xy(xy, type,...
Needs docs and a decision if this is the way to proceed or if we need to make `prep` sparse-friendly. Fixes #7
I work with binary data a lot and I like the nipals approach. Would you be open to adaptions of pcaMethods::nipalsPca to do MCA instead of PCA? I had a...
