How to run combat-seq, strange output?
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2 days ago
Maryam • 0

I ran the combat-seq for my data

The full program was executed, but its output is as follows

I checked the code several times and I do not know where the problem is

Can you help?

files <-list.files(".","*.count")
cnt <- lapply(files,read.delim,header=F)
cnt<- lapply(files,read.delim,header=F,stringsAsFactors=F)
cnt<-do.call(cbind,cnt)
cnt<- cnt[,-seq(1,ncol(cnt),2)]
colnames(cnt)<- sub(".count","",files)
batch<- samplerace
samplecondition <- factor(rep(c('control','control','fibrosis','fibrosis'),84))
covariate_matrix = cbind(group,samplegender)
cntcombat<-ComBat_seq(cnt,batch= batch,full_mod=TRUE,group=NULL, 
                      covar_mod = covariate_matrix)


 head(cntcombat)
[[1]]
[1] 50

[[2]]
[1] 11

[[3]]
   [1] 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
  [70] 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [139] 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [208] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
 [277] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 2 0 0 2 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
combat-seq effect R batch • 126 views
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Please show examples of the counts and the design.

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thanks

head(cnt)
          V2 V2.1 V2.2 V2.3 V2.4 V2.5 V2.6 V2.7 V2.8 V2.9 V2.10 V2.11 V2.12 V2.13 V2.14 V2.15 V2.16 V2.17 V2.18 V2.19 V2.20 V2.21 V2.22 V2.23
A1BG       0    4    3    2    6    0    1    0    1    9     4     2     0     4     3     4     4     5     4     2     2     2     4     2
A1BG-AS1   1    4   14    1    3    0    2    5    7    1     4     4     7     3     4     8    10    11     6     3     4     4    18     6
A1CF       1    1    1    2    0    0    4    2    0    1     0     2     1     3     0     2     2     0     2     1     0     0     3     1
A2M      147   51   98   67   85   61   72   53   67   64    76    49    63    61    48    69    58    52    82    39    48     8   114    57
A2M-AS1  906 1100  987  647  968 1068  887 1022 1017 1154  1226   956  1085  1387  1392  1086   832  1565  1110  1251   642    95  2501  1234
A2ML1      4    2    3    2    3    6    1    0    2    2     5     1     5     1     1     2     2     3     3     0     2     0     1     3
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