Hi every one,
I use Hmisc package to calculate the correlation, my input file is expression matrix, (gene names in row and samples in the column), the result of the analysis contains 4 columns, (two columns are the name of the genes, a cor column, and p-value column). When the repetitions of each group are less than 4, I encounter the following error:
Error in rcorr(control) : must have >4 observations
My study groups have two replications, are there any method or package that output file similar to the Hmisc package? Thanks a lot.
1 answer
rcorr computes correlations between the columns of the input matrix so if your genes are in rows and samples in columns, you're computing the correlations between samples. As for the error, you're getting it because although it is possible to compute a correlation with fewer values, it doesn't make much sense. For n = 2, the correlation is either -1 or +1 (you can always draw a line between two points) and in general, for low n, it may make you think that a linear relation exists when there is none.
Log in to answer this question.
-
t-test by row
written by sooni •
-
Calculating correlation matrix with multiple observations per observable
written by bioneer •
-
A chord plot for miRNA IDs by GOplot package
written by Morteza Hadizadeh •
-
space converted into dots in header name
written by Bioinfonext
-
How to calculate Spearman correlation coefficient and p-values between numeric and non-numeric data…
written by prithvi.mastermind •
-
Pearson's Correlation Coefficient and expression matrix
written by Morteza Hadizadeh •
-
Remove batch effects in meta-analysis
written by Morteza Hadizadeh •
-
question about co-expression in TCGA
written by tujuchuanli
-
Gene-gene Pearson Correlation
written by pixie@bioinfo
-
Computing T-Test For Genes With Help Of Apply Function
written by jack •
