Problem in analysing microarray data with ComBat
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@melissasorci-7969
Last seen 6.4 years ago
European Union

I'm having problems with ComBat. I did a csv sample information file according to on line instruction. But every time I got this Error message:

"ERROR: Sample Information File does not have a Batch column!"

I don't understand what is going on as the Batch column is in the file. I have also tried to use txt files but in that case I got a different error message:

"ERROR: Array expression columns contain non-numeric values! (Check your .xls file for non-numeric values and if this is not the problem, make a .csv file and use the type=csv option)"

I hope you can help me.

Thank you very much

Sincerely 

combat • 955 views
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Please show the top couple lines of your csv file to help in troubleshooting, also what version of ComBat are you running (the function in SVA library?). You need to specify a batch categorical variable that corresponds to the effect you are trying to remove.
 

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@melissasorci-7969
Last seen 6.4 years ago
European Union

I understand the error messages, now ComBat is able to read my files but than it gives me this other error message:

Reading Sample Information File
Reading Expression Data File
Found 104 batches
Found 1 covariate(s)

 Error in `[<-`(`*tmp*`, , i, value = c(NA, NA, NA, NA, NA, NA, NA, NA,  : 
  subscript out of bounds 

I don't know how to solve the problem! Thank you very much!

Melissa

 

 

 

 

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it looks like you are having a mismatch between number of rows that combat is reading in with the number of data rows that you have, you probably also want to check why the value is NA

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