Question

Problem in analysing microarray data with ComBat

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melissa.sorci • 0

@melissasorci-7969

Last seen 9.5 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 • 1.9k views

ADD COMMENT • link updated 20 months ago by W. Evan Johnson ▴ 870 • written 9.5 years ago by melissa.sorci • 0

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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.

ADD REPLY • link 9.5 years ago Ying W ▴ 90

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I ran into the same problem as Melissa: "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 am using the old (standalone) version of the ComBat (not the function in the sva package). I tried both .txt and .csv but got the same error message. I believe all the expression values in my file are numeric (I even formatted all the cells to Number in Excel). Below is a snippet of the top left corner of my expression file.

Snippet

Please help to identify where the problem is. Thank you very much for your help!

Xiugong

ADD REPLY • link 20 months ago xgao • 0

score 0 · Answer 1 · 2015-05-29

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melissa.sorci • 0

@melissasorci-7969

Last seen 9.5 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

ADD COMMENT • link 9.5 years ago melissa.sorci • 0

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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

ADD REPLY • link 9.5 years ago Ying W ▴ 90

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Hi Melissa,

Could you let me know how did you solve the problem of the expression file? Please refer to my comment above.

Thank you,

Xiugong

ADD REPLY • link 20 months ago xgao • 0

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Xiugong, I believe she was using the ComBat.R script, you should now be using the ComBat function in the sva package. Give that a try and let me know if you run into any problems!

ADD REPLY • link 20 months ago W. Evan Johnson ▴ 870