Normalized count or Count data for ToPASeq package
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@saamarrajput-10623
Last seen 8.4 years ago

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?

 

 

rnaseq Topaseq • 1.5k views
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Make sure you are passing a matrix.

as.matrix(CountData)

 

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@mikelove
Last seen 14 hours ago
United States
You should tag this post with the name of the package to get feedback from the maintainer.
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