Hi,
I am trying to implement the Windows-friendly version of CytofBatchAdjust to batch correct my data. Following the ReadMe and HowTo, I have managed to make the algorithm generate "corrected" files (in parentheses because i haven't imported the files into a gating software to check yet).
My non-anchor files are named "Batch[##]_xxx.fcs" and my anchor files are named "Batch[##]_Anchor_Pos_xxx.fcs".
I have my .fcs files, the BatchAdjust.R code, and ChannelsToAdjust.txt in a folder titled "FCS_Files", and the "BatchAdjust()" function is set up as follows:
BatchAdjust(
basedir=".",
outdir="TheSameParentDirectoryAsForTheBasedirFolder/FCS_Files_Corrected",
channelsFile = "ChannelsToAdjust.txt",
batchKeyword="Batch",
anchorKeyword = "Anchor_Pos",
method="95p",
transformation=FALSE,
addExt="_Corrected",
plotDiagnostics=TRUE)
However, the final output in the console is: "[1] Testing total variance reduction:", after which the following error is shown:
Error in totalVar_allEvents(predir = basedir, postdir = outdir, batchKeyword = batchKeyword, :
totalVar_allEvents: File names in pre and post directories don't match.
I have gone through the code step by step and cannot manage to discern the cause of the issue.
I have managed to bypass the error by setting both the basedir and outdir to "." and removing the following lines of code at the same time:
if (dir.exists(outdir))
stop("outdir \'", outdir, "\' already exists. It cannot be overwritten.")
...but then I get marker intensity distribution histograms that repeat over each other twice.
Luka
Hi,
I am trying to implement the Windows-friendly version of CytofBatchAdjust to batch correct my data. Following the ReadMe and HowTo, I have managed to make the algorithm generate "corrected" files (in parentheses because i haven't imported the files into a gating software to check yet).
My non-anchor files are named "Batch[##]_xxx.fcs" and my anchor files are named "Batch[##]_Anchor_Pos_xxx.fcs".
I have my .fcs files, the BatchAdjust.R code, and ChannelsToAdjust.txt in a folder titled "FCS_Files", and the "BatchAdjust()" function is set up as follows:
However, the final output in the console is: "[1] Testing total variance reduction:", after which the following error is shown:
I have gone through the code step by step and cannot manage to discern the cause of the issue.
I have managed to bypass the error by setting both the basedir and outdir to "." and removing the following lines of code at the same time:
...but then I get marker intensity distribution histograms that repeat over each other twice.
Luka