Hello,
I'm a NIH scientists that is doing a HTS experiment and I'm using your Cell HTS2 software to analyze our results.
I'm doing two different experiments with 2 repeats for each of them. I want to combine the results and thought to try the batch function.
Currently, I'm doing per plate normalization and no variance adjustment. I would like to do batch variance adjust, but I'm uncertain as to what this will do to the normalized results. Could you please provide me with a general explanation of variance adjustment, what it does and why?
Additionally, when I add the batch number to the plate list and ask the program to do a variance adjust by batch, we get the following error:

> x <- configure(x,
+                descripFile="Description.txt",
+                confFile="Plateconf.txt",
+                path=dataPath)
> xn <- normalizePlates(x,
+                       scale="multiplicative",
+                       log=FALSE,
+                       method="median",
+                       varianceAdjust="byBatch")

Error in adjustVariancebyBatch(<S4 object of class "cellHTS">) :
  'batch' should have dimensions 'Features x Samples x Channels' (768 x 4 x 1).
In addition: Warning message:
In dim(bb) != d :
  longer object length is not a multiple of shorter object length

The error is not in the platelist file because the program identifies the different batches:

> batch(x)
       replicate1 replicate2 replicate3 replicate4
plate1          1          1          2          2
plate2          1          1          2          2

Could you help me solve this error?

Also, please add any example scripts of a variance adjustment by batch and an explanation.
Thank you in advance,
Keren Baranes Bachar
NCI/NIH

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