Hi Keren,
I finally found some time to fix the batch issue in cellHTS2. Things 
should work fine now in both the updated release version (2.10.1) and the 
latest devel version (2.11.1)
Thanks again for the notice and let me know if you encounter other 
problems.
Florian





"Baranes-Bachar, Keren (NIH/NCI) [V]" <baranesbacharkg@mail.nih.gov> 
Sent by: bioconductor-bounces@stat.math.ethz.ch
21.10.2009 18:58

To
"'bioconductor@stat.math.ethz.ch'" <bioconductor@stat.math.ethz.ch>
cc

Subject
[BioC] batch info for cellHTS2






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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