Hi All,
I am using the ToPASeq package for pathway analysis for my RNASe data for host and pathogen simultaneoulsy. I used htseq-counts to get the counts against each gene after mapping for both the host and pathogen RNASeq data. then I tried to merge the samples to make a count data file for the input for ToPASeq
top<-TopologyGSA(CountData, group,pathways, type="RNASeq")
but it gave me the error
Error in processRNAseq(x, group, norm.method) :
Integer count data expected
It also takes in normalized counts as input so i Used DESeq2 to get the normalized counts and tried using this file as input for ToPASeq but it stii gives me the same error.
Error in processRNAseq(x, group, norm.method) :
Integer count data expected
Although i checked my files and they are all integers for the count data file and decimals for normalized count.
| M21 | M22 | M23 | M41 | M42 | M43 | M81 | M82 | M83 | M161 | M162 | M163 | M241 | M242 | M243 | W01 | W02 | W03 | W21 | W22 | W23 | W41 | W42 | W43 | W81 | W82 | W83 | W161 | W162 | W163 | W241 | W242 | W243 | |
| NONHSAG000001.1 | 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 |
| NONHSAG000001.2 | 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 |
| NONHSAG000002.1 | 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 |
| NONHSAG000002.2 | 2 | 1 | 14 | 2 | 2 | 9 | 24 | 1 | 6 | 3 | 0 | 6 | 5 | 1 | 12 | 1 | 5 | 10 | 2 | 3 | 31 | 1 | 0 | 18 | 0 | 0 | 14 | 5 | 0 | 3 | 0 | 4 | 0 |
| NONHSAG000003.1 | 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 |
my count data file looks like this
| GeneCount_M161 | GeneCount_M162 | GeneCount_M163 | GeneCount_M21 | GeneCount_M22 | GeneCount_M23 | GeneCount_M241 | GeneCount_M242 | GeneCount_M243 | GeneCount_M41 | GeneCount_M42 | GeneCount_M43 | GeneCount_M81 | GeneCount_M82 | GeneCount_M83 | GeneCount_W01 | GeneCount_W02 | GeneCount_W03 | GeneCount_W161 | GeneCount_W162 | GeneCount_W163 | GeneCount_W21 | GeneCount_W22 | GeneCount_W23 | GeneCount_W241 | GeneCount_W242 | GeneCount_W243 | GeneCount_W41 | GeneCount_W42 | GeneCount_W43 | GeneCount_W81 | GeneCount_W82 | GeneCount_W83 | |
| NONHSAG000001.1 | 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 |
| NONHSAG000001.2 | 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 |
| NONHSAG000002.1 | 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 |
| NONHSAG000002.2 | 3.6593382827 | 0 | 3.4148139255 | 1.4314753134 | 0.6178873618 | 7.5946588042 | 4.5876310195 | 1.9155117281 | 7.8475096087 | 1.4083226492 | 1.1090612857 | 6.6849601076 | 10.536249353 | 1.2694915189 | 3.6707055573 | 0.6749264903 | 2.7894828796 | 4.2007627555 | 5.0961685616 | 0 | 3.585271828 | 1.5802707724 | 2.2243208788 | 23.028852408 | 0 | 3.6211040787 | 0 | 0.6363530409 | 0 | 12.5510389762 | 0 | 0 | 6.9661105882 |
| NONHSAG000003.1 | 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 |
and normalized counts look like this
can somebody help me?
Make sure you are passing a matrix.
as.matrix(CountData)