Question: error in running Combat function
0
gravatar for reza
13 days ago by
reza240
Iran
reza240 wrote:

I run the same commands on the same data in Rstudio in Windows and Linux, but I get different results in step removing batch effect using “Combat” function (sva package). Running “Combat” on Windows is error-free, while on Linux I get the following error:

Error in ((dat - t(design %*% B.hat))^2) %*% rep(1/n.array, n.array) : 
requires numeric/complex matrix/vector arguments

Commands

all <- read.delim("All.txt", header = T, row.names = 1) 
allm <- all - rowMeans(all)
pc <- prcomp(allm)
Sets <- (c(rep("GSExxx", 30), rep("GSExxxx", 12), rep("GSExx", 14), rep("GSEx", 12)))
pcr <- data.frame(pc$r[,1:3], Sets)
allc <- ComBat(all, Sets)

how can solve this problem?

Thanks for your helps

combat sva R r studio • 84 views
ADD COMMENTlink written 13 days ago by reza240

Hello, can you please provide a minumal data example for the relevant variables that allows reproduction of the error, for example via the dput() function?

ADD REPLYlink written 13 days ago by ATpoint44k

how can I do that using dput() function?

ADD REPLYlink written 13 days ago by reza240

For example dput(head(all)) would give you a text representation that you can copy/paste of the all variable. Please provide example data for Sets and all.

ADD REPLYlink written 13 days ago by ATpoint44k
 Sets <- (c(rep("GSEx", 12), rep("GSExx", 12), rep("GSExxx", 9), rep("GSExxxx", 13)))

AND

> dput(head(all))
structure(list(A1 = c(6.9381, 7.5079, 7.2303, 8.9908, 8.2564, 
11.0564), A2 = c(6.9594, 7.3883, 7.1023, 8.9328, 8.1679, 10.8513
), A3 = c(6.8419, 7.2109, 6.9548, 8.7414, 8.0299, 10.8115), A4 = c(6.6619, 
7.1364, 6.887, 8.6863, 8.006, 10.8775), A5 = c(6.9296, 7.2845, 
7.0382, 8.8176, 8.1234, 10.9084), A6 = c(7.1549, 7.5539, 7.2842, 
9.0999, 8.3527, 11.1642), A7 = c(6.6192, 7.1043, 6.9482, 8.6802, 
7.9977, 10.7216), A8 = c(7.2778, 7.6654, 7.3542, 9.2437, 8.5063, 
11.2892), A9 = c(7.282, 7.5827, 7.3097, 9.116, 8.4326, 11.1977
), A10 = c(7.3402, 7.7757, 7.4926, 9.2278, 8.6172, 11.1968), 
    A11 = c(6.6635, 7.1918, 6.8924, 8.6318, 7.9105, 10.7312), 
    A12 = c(6.8926, 7.3513, 6.9834, 8.7605, 8.0945, 10.8734), 
    B1 = c(6.8014, 7.1908, 6.8015, 8.8403, 8.0259, 10.7076), 
    B2 = c(6.5855, 7.1594, 6.6593, 8.7153, 7.9119, 10.7066), 
    B3 = c(6.4392, 7.0688, 6.5803, 8.6158, 7.8153, 10.6042), 
    B4 = c(6.7046, 7.078, 6.7047, 8.6752, 7.8961, 10.6192), B5 = c(7.9128, 
    8.3322, 8.0958, 9.8519, 8.9967, 11.6034), B6 = c(6.9226, 
    7.4705, 7.1007, 8.9497, 8.2543, 10.711), B7 = c(6.421, 7.0791, 
    6.4662, 8.5758, 7.7724, 10.5219), B8 = c(6.4972, 7.1769, 
    6.7016, 8.7424, 7.9157, 10.7647), B9 = c(6.6425, 7.3366, 
    6.5679, 8.8394, 7.9696, 10.7032), B10 = c(6.3134, 6.7753, 
    6.4695, 8.4463, 7.644, 10.5063), B11 = c(6.4938, 7.0694, 
    6.336, 8.6302, 7.688, 10.5626), B12 = c(6.2451, 6.9604, 6.2342, 
    8.4628, 7.6297, 10.5476), C1 = c(4.9469, 5.1746, 5.1522, 
    9.5331, 8.9385, 11.4915), C2 = c(5.0953, 5.1003, 5.2505, 
    9.6333, 9.0602, 11.4867), C3 = c(5.0583, 5.0543, 5.1091, 
    9.6526, 9.0479, 11.5055), C4 = c(4.9402, 5.1395, 5.2561, 
    9.655, 9.0221, 11.5286), C5 = c(5.0406, 5.1575, 5.2761, 9.6413, 
    9.0673, 11.5767), C6 = c(4.9726, 5.3945, 5.1122, 9.5541, 
    9.0265, 11.5038), C7 = c(5.3879, 5.1028, 5.0608, 9.803, 9.2769, 
    11.8283), C8 = c(5.127, 5.142, 5.1496, 9.9158, 9.2543, 11.8024
    ), C9 = c(5.3067, 5.1215, 5.0303, 9.9562, 9.3744, 11.8254
    ), D1 = c(7.0772, 7.4086, 7.2877, 9.0927, 8.6348, 11.2268
    ), D2 = c(6.6349, 7.0915, 6.6813, 8.5535, 8.1593, 10.9012
    ), D3 = c(7.4336, 7.7217, 7.512, 9.3543, 8.8803, 11.5023), 
    D4 = c(7.4971, 7.8568, 7.672, 9.441, 9.0128, 11.6245), D5 = c(7.2505, 
    7.5549, 7.3561, 9.2116, 8.6796, 11.3779), D6 = c(6.8906, 
    7.2358, 7.054, 8.8379, 8.4158, 11.0953), D7 = c(6.6697, 7.0378, 
    6.9185, 8.7005, 8.1895, 11.0119), D8 = c(6.955, 7.2885, 7.1322, 
    8.922, 8.4309, 11.1848), D9 = c(7.4286, 7.628, 7.5056, 9.2589, 
    8.8542, 11.5108), D10 = c(7.1027, 7.3881, 7.2015, 9.0158, 
    8.5069, 11.2525), D11 = c(6.9174, 7.2366, 7.1286, 8.8789, 
    8.5092, 11.1913), D12 = c(7.3573, 7.6144, 7.4158, 9.231, 
    8.7868, 11.4215), D13 = c(7.3078, 7.5243, 7.4756, 9.2333, 
    8.7521, 11.4136)), row.names = c("AFFX-BioB-3_at", "AFFX-BioB-5_at", 
"AFFX-BioB-M_at", "AFFX-BioC-3_at", "AFFX-BioC-5_at", "AFFX-BioDn-3_at"
), class = "data.frame")
ADD REPLYlink written 12 days ago by reza240

Dear ATpoint, you have no advice to solve this error?

ADD REPLYlink written 11 days ago by reza240

The code runs without error on my machine (macOS 10.14). I suggest you post this over at support.bioconductor.org using the sva tag and hope that the developers can help.

ADD REPLYlink written 11 days ago by ATpoint44k
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