Hi,

I am a newbie in R and hope you can help me in processing the data I have.
So, there we go:

I am trying to reduce batch effect in my samples, coming from a mass
spectrometry background.

sva and other packages are installed and loaded. My data file structure
looks like this:

   *Array Name* *Sample Name* *Batch* *Class* *Age* *Gender*  *1_103C* *103C
* *1* *Control* *6* *M*  *1_104C* *104C* *1* *Control* *6* *M*  *1_107C* *
107C* *1* *Control* *6* *M*  *1_108C* *108C* *1* *Control* *6* *F*  *1_10C*
*10C* *1* *Control* *6* *M*  *1_11* *11* *1* *ECA* *7* *M*  *1_114C* *114C*
*1* *Control* *6* *F*  *1_117C* *117C* *1* *Control* *6* *M*  *1_11C* *11C*
*1* *Control* *6* *M*  *1_12* *12* *1* *ECA* *7* *M*  *1_12C* *12C* *1* *
Control* *6* *M*
The syntax line looks like this:

*Combat_ECA=ComBat(dat=Dataset1 , batch=batch , mod=mod , numCovs=NULL ,
par.prior=FALSE)
*
However, when I run it this is what I get:

*"Found 2 batches
Found 2  categorical covariate(s)
Found 2334 Missing Data Values
Standardizing Data across genes
Error in FUN(newX[, i], ...) : (subscript) logical subscript too long"*

And then it halts.
When I do a traceback, this is what I get:
*
3: FUN(newX[, i], ...)
2: apply(dat, 1, Beta.NA, design)
1: ComBat(dat = Dataset1, batch = batch, mod = mod, numCovs = NULL,
       par.prior = FALSE)*

 I am not sure if I get this error message because of missing data or
something is wrong with my data structure. I could not find much on this
error message and how to correct it. Would you please help me with this?
Let me know if more details are needed.

Thanks,
Farshad

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