For loop paired to t tests returning matrix error
1
I have a large set of data frames and would like to conduct a series of t-tests between different columns to find significance. Each data frame has identical headers but a different number of rows.
This is my code:
fileNames <- Sys.glob("*.txt")
for (fileName in fileNames) {
sample <- read.delim(fileName)
print(fileName)
placeholder.1 <- row_t_welch(sample[,c("A284_1", "A284_2")], sample[,c("A285_1", "A285_2")
}
Where fileNames = a list of: chr [1:383], and _1 & _2 are biological replicates
My code returns the error:
Error in assert_numeric_mat_or_vec(x):
"x" must be a numeric matrix or vector
If I type in the name of the files individually the code works but not when using 'sample'
Can anyone help me?
This is an excerpt from one of my files
seq seq_id A284_1 A284_2 A285_1 A285_2 A286_1 A286_2 A287_1 A287_2 A288_1 A288_2 A289_1 A289_2 A290_1 A290_2 A291_1 A291_2 N2_1 N2_2
1 0.0345 0.0025 0.0134 0.0000 0.0114 0.0064 0.0011 0.0000 0.0000 0.0000 0.0000 0.0132 0.0094 0.0076 0.0000 0.0000 0.0023 0.0213 0.0130 0.0101
2 0.0394 0.0049 0.0015 0.0000 0.0011 0.0010 0.0000 0.0000 0.0015 0.0022 0.0013 0.0014 0.0011 0.0009 0.0000 0.0000 0.0021 0.0014 0.0013 0.0007
3 0.0296 0.0074 0.0000 0.0000 0.0008 0.0005 0.0011 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0038 0.0000 0.0000 0.0003 0.0014 0.0050 0.0032
4 0.0197 0.0099 0.0059 0.0015 0.0030 0.0044 0.0011 0.0075 0.0015 0.0022 0.0017 0.0023 0.0022 0.0023 0.0000 0.0054 0.0027 0.0014 0.0022 0.0022
5 0.0099 0.0123 0.0045 0.0046 0.0038 0.0049 0.0076 0.0000 0.0030 0.0067 0.0039 0.0054 0.0039 0.0067 0.0051 0.0054 0.0071 0.0071 0.0060 0.0052
r matrix vector t-test
asked Jan 2 at 23:50
A. PalmerA. Palmer
93
add a comment |
1
I have a large set of data frames and would like to conduct a series of t-tests between different columns to find significance. Each data frame has identical headers but a different number of rows.
This is my code:
fileNames <- Sys.glob("*.txt")
for (fileName in fileNames) {
sample <- read.delim(fileName)
print(fileName)
placeholder.1 <- row_t_welch(sample[,c("A284_1", "A284_2")], sample[,c("A285_1", "A285_2")
}
Where fileNames = a list of: chr [1:383], and _1 & _2 are biological replicates
My code returns the error:
Error in assert_numeric_mat_or_vec(x):
"x" must be a numeric matrix or vector
If I type in the name of the files individually the code works but not when using 'sample'
Can anyone help me?
This is an excerpt from one of my files
seq seq_id A284_1 A284_2 A285_1 A285_2 A286_1 A286_2 A287_1 A287_2 A288_1 A288_2 A289_1 A289_2 A290_1 A290_2 A291_1 A291_2 N2_1 N2_2
1 0.0345 0.0025 0.0134 0.0000 0.0114 0.0064 0.0011 0.0000 0.0000 0.0000 0.0000 0.0132 0.0094 0.0076 0.0000 0.0000 0.0023 0.0213 0.0130 0.0101
2 0.0394 0.0049 0.0015 0.0000 0.0011 0.0010 0.0000 0.0000 0.0015 0.0022 0.0013 0.0014 0.0011 0.0009 0.0000 0.0000 0.0021 0.0014 0.0013 0.0007
3 0.0296 0.0074 0.0000 0.0000 0.0008 0.0005 0.0011 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0038 0.0000 0.0000 0.0003 0.0014 0.0050 0.0032
4 0.0197 0.0099 0.0059 0.0015 0.0030 0.0044 0.0011 0.0075 0.0015 0.0022 0.0017 0.0023 0.0022 0.0023 0.0000 0.0054 0.0027 0.0014 0.0022 0.0022
5 0.0099 0.0123 0.0045 0.0046 0.0038 0.0049 0.0076 0.0000 0.0030 0.0067 0.0039 0.0054 0.0039 0.0067 0.0051 0.0054 0.0071 0.0071 0.0060 0.0052
r matrix vector t-test
asked Jan 2 at 23:50
A. PalmerA. Palmer
93
read.delim()returns adata.framewhereas you require a matrix. Try converting it to a matrix.
– anotherfred
Jan 2 at 23:57
Please don't include images of your data. Include the output fromdput(head(data))or a simple made-up example that we can copy/paste into R
– RAB
Jan 3 at 1:13
Thankyou @anotherfred! It now works. What I did was insertsample <- data.matrix(sample)undersample <- read.delim(fileName)andprint(placeholder.1)underneath my statistical test. This was as calling theplaceholder.1variable returned a null result
– A. Palmer
Jan 3 at 1:45
add a comment |
1
1
1
I have a large set of data frames and would like to conduct a series of t-tests between different columns to find significance. Each data frame has identical headers but a different number of rows.
This is my code:
fileNames <- Sys.glob("*.txt")
for (fileName in fileNames) {
sample <- read.delim(fileName)
print(fileName)
placeholder.1 <- row_t_welch(sample[,c("A284_1", "A284_2")], sample[,c("A285_1", "A285_2")
}
Where fileNames = a list of: chr [1:383], and _1 & _2 are biological replicates
My code returns the error:
Error in assert_numeric_mat_or_vec(x):
"x" must be a numeric matrix or vector
If I type in the name of the files individually the code works but not when using 'sample'
Can anyone help me?
This is an excerpt from one of my files
seq seq_id A284_1 A284_2 A285_1 A285_2 A286_1 A286_2 A287_1 A287_2 A288_1 A288_2 A289_1 A289_2 A290_1 A290_2 A291_1 A291_2 N2_1 N2_2
1 0.0345 0.0025 0.0134 0.0000 0.0114 0.0064 0.0011 0.0000 0.0000 0.0000 0.0000 0.0132 0.0094 0.0076 0.0000 0.0000 0.0023 0.0213 0.0130 0.0101
2 0.0394 0.0049 0.0015 0.0000 0.0011 0.0010 0.0000 0.0000 0.0015 0.0022 0.0013 0.0014 0.0011 0.0009 0.0000 0.0000 0.0021 0.0014 0.0013 0.0007
3 0.0296 0.0074 0.0000 0.0000 0.0008 0.0005 0.0011 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0038 0.0000 0.0000 0.0003 0.0014 0.0050 0.0032
4 0.0197 0.0099 0.0059 0.0015 0.0030 0.0044 0.0011 0.0075 0.0015 0.0022 0.0017 0.0023 0.0022 0.0023 0.0000 0.0054 0.0027 0.0014 0.0022 0.0022
5 0.0099 0.0123 0.0045 0.0046 0.0038 0.0049 0.0076 0.0000 0.0030 0.0067 0.0039 0.0054 0.0039 0.0067 0.0051 0.0054 0.0071 0.0071 0.0060 0.0052
r matrix vector t-test
asked Jan 2 at 23:50
A. PalmerA. Palmer
93
I have a large set of data frames and would like to conduct a series of t-tests between different columns to find significance. Each data frame has identical headers but a different number of rows.
This is my code:
fileNames <- Sys.glob("*.txt")
for (fileName in fileNames) {
sample <- read.delim(fileName)
print(fileName)
placeholder.1 <- row_t_welch(sample[,c("A284_1", "A284_2")], sample[,c("A285_1", "A285_2")
}
Where fileNames = a list of: chr [1:383], and _1 & _2 are biological replicates
My code returns the error:
Error in assert_numeric_mat_or_vec(x):
"x" must be a numeric matrix or vector
If I type in the name of the files individually the code works but not when using 'sample'
Can anyone help me?
This is an excerpt from one of my files
seq seq_id A284_1 A284_2 A285_1 A285_2 A286_1 A286_2 A287_1 A287_2 A288_1 A288_2 A289_1 A289_2 A290_1 A290_2 A291_1 A291_2 N2_1 N2_2
1 0.0345 0.0025 0.0134 0.0000 0.0114 0.0064 0.0011 0.0000 0.0000 0.0000 0.0000 0.0132 0.0094 0.0076 0.0000 0.0000 0.0023 0.0213 0.0130 0.0101
2 0.0394 0.0049 0.0015 0.0000 0.0011 0.0010 0.0000 0.0000 0.0015 0.0022 0.0013 0.0014 0.0011 0.0009 0.0000 0.0000 0.0021 0.0014 0.0013 0.0007
3 0.0296 0.0074 0.0000 0.0000 0.0008 0.0005 0.0011 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0038 0.0000 0.0000 0.0003 0.0014 0.0050 0.0032
4 0.0197 0.0099 0.0059 0.0015 0.0030 0.0044 0.0011 0.0075 0.0015 0.0022 0.0017 0.0023 0.0022 0.0023 0.0000 0.0054 0.0027 0.0014 0.0022 0.0022
5 0.0099 0.0123 0.0045 0.0046 0.0038 0.0049 0.0076 0.0000 0.0030 0.0067 0.0039 0.0054 0.0039 0.0067 0.0051 0.0054 0.0071 0.0071 0.0060 0.0052
r matrix vector t-test
r matrix vector t-test
asked Jan 2 at 23:50
A. PalmerA. Palmer
93
asked Jan 2 at 23:50
A. PalmerA. Palmer
93
edited Jan 3 at 2:00
A. Palmer
asked Jan 2 at 23:50
A. PalmerA. Palmer
93
asked Jan 2 at 23:50
A. PalmerA. Palmer
93
asked Jan 2 at 23:50
A. PalmerA. Palmer
93
93
read.delim()returns adata.framewhereas you require a matrix. Try converting it to a matrix.
– anotherfred
Jan 2 at 23:57
Please don't include images of your data. Include the output fromdput(head(data))or a simple made-up example that we can copy/paste into R
– RAB
Jan 3 at 1:13
Thankyou @anotherfred! It now works. What I did was insertsample <- data.matrix(sample)undersample <- read.delim(fileName)andprint(placeholder.1)underneath my statistical test. This was as calling theplaceholder.1variable returned a null result
– A. Palmer
Jan 3 at 1:45
add a comment |
read.delim()returns adata.framewhereas you require a matrix. Try converting it to a matrix.
– anotherfred
Jan 2 at 23:57
Please don't include images of your data. Include the output fromdput(head(data))or a simple made-up example that we can copy/paste into R
– RAB
Jan 3 at 1:13
Thankyou @anotherfred! It now works. What I did was insertsample <- data.matrix(sample)undersample <- read.delim(fileName)andprint(placeholder.1)underneath my statistical test. This was as calling theplaceholder.1variable returned a null result
– A. Palmer
Jan 3 at 1:45
read.delim() returns a data.frame whereas you require a matrix. Try converting it to a matrix.– anotherfred
Jan 2 at 23:57
read.delim() returns a data.frame whereas you require a matrix. Try converting it to a matrix.– anotherfred
Jan 2 at 23:57
Please don't include images of your data. Include the output from
dput(head(data)) or a simple made-up example that we can copy/paste into R– RAB
Jan 3 at 1:13
Please don't include images of your data. Include the output from
dput(head(data)) or a simple made-up example that we can copy/paste into R– RAB
Jan 3 at 1:13
Thankyou @anotherfred! It now works. What I did was insert
sample <- data.matrix(sample) under sample <- read.delim(fileName) and print(placeholder.1) underneath my statistical test. This was as calling the placeholder.1 variable returned a null result– A. Palmer
Jan 3 at 1:45
Thankyou @anotherfred! It now works. What I did was insert
sample <- data.matrix(sample) under sample <- read.delim(fileName) and print(placeholder.1) underneath my statistical test. This was as calling the placeholder.1 variable returned a null result– A. Palmer
Jan 3 at 1:45
add a comment |
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read.delim()returns adata.framewhereas you require a matrix. Try converting it to a matrix.– anotherfred
Jan 2 at 23:57
Please don't include images of your data. Include the output from
dput(head(data))or a simple made-up example that we can copy/paste into R– RAB
Jan 3 at 1:13
Thankyou @anotherfred! It now works. What I did was insert
sample <- data.matrix(sample)undersample <- read.delim(fileName)andprint(placeholder.1)underneath my statistical test. This was as calling theplaceholder.1variable returned a null result– A. Palmer
Jan 3 at 1:45