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Hello,
I am trying to do Batch correction using SVA package (with ComBat function) for my RNA-seq raw counts data.
When performing step 4: Applying the sva fuction, I found an error message like this:
Because my raw counts data have many genes show zero expression, I then removed those lines with zero. And I also removed batches that had only one sample each. Then this error message was still there. But I can go ahead with step 7: Applying the ComBat function and get the adjusted data.
I wonder if it correct that I remove those lines with zero.
my original expression data looks like this:
I am trying to do Batch correction using SVA package (with ComBat function) for my RNA-seq raw counts data.
When performing step 4: Applying the sva fuction, I found an error message like this:
PHP Code:
> n.sv = num.sv(edata2,mod,method="leek")
> n.sv
[1] 14
> svobj = sva(edata2,mod,mod0,n.sv=n.sv)
Number of significant surrogate variables is: 14
Iteration (out of 5 ):Error in density.default(x, adjust = adj) : 'x' contains missing values
In addition: Warning message:
In pf(fstats, df1 = (df1 - df0), df2 = (n - df1)) : NaNs produced
Error during wrapup: cannot open the connection
I wonder if it correct that I remove those lines with zero.
my original expression data looks like this:
PHP Code:
> head(edata)
FH1.B2.K100813 FH0.B3.K100823 FH1.B2.K100826 FH1.B2.K100831 FH0.B2.K101448 FH0.B2.K102654 FH0.B5.K104200 FH0.B5.K104238 FH0.B2.K104250 FH0.B2.K104343 FH0.B3.K104403 FH0.B5.K104443
40969 69.00 11.00 4.00 55.00 78.67 138.00 109.00 70.00 144.00 127.92 118.00 57.00
40970 569.43 73.22 6.00 534.51 153.15 400.14 351.60 440.97 127.28 214.97 106.65 455.01
40974 1647.12 150.30 51.58 1932.85 1018.62 1039.99 2019.72 2080.37 1634.20 847.77 882.49 1834.79
ADAM23 5.01 0.00 0.00 4.96 32.00 0.00 33.00 19.91 30.01 10.01 23.00 9.92
ASNS 91.39 31.00 6.00 99.32 157.44 130.71 176.98 76.58 290.99 113.38 127.00 101.89
C14ORF10 14.01 4.07 0.00 32.78 15.74 8.29 22.71 31.55 19.09 18.76 7.58 19.44
FH1.B5.K104506 FH0.B2.K104603 FH0.B2.K104638 FH1.B2.K104824
40969 120.00 191.00 56.00 58.00
40970 550.40 764.77 310.11 329.31
40974 1742.01 2296.24 1081.09 911.42
ADAM23 19.91 39.98 20.02 4.98
ASNS 84.12 89.83 63.28 95.25
C14ORF10 13.40 29.57 15.75 11.14
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