Question: Goseq pwf nullp error
0
gravatar for Gerde
4.4 years ago by
Gerde0
China
Gerde0 wrote:

Hi all,

      I got some trouble while use goseq to do enrichment analysis recently, the trouble is :

> pwf=nullp(de.data,bias.data=gene.length)
Error in if (min(fv) < lower_bound) fv = fv - min(fv) + lower_bound :
  missing value where TRUE/FALSE needed

while using nullp function to calculate probability weight, I get the errors, could somebody help me?

ps: no "NA" existed in dataframe "de.data",  length(de.data) == length(gene.length)

Thanks a lot!

pwf rna-seq R • 2.2k views
ADD COMMENTlink modified 4.3 years ago • written 4.4 years ago by Gerde0

What is your organism? How are you producing gene.length?

ADD REPLYlink written 4.3 years ago by Parham1.4k

Hi Parham, sorry for my delay, the organism is sheep, and the gene.length is as below:

gi|426215078|ref|XM_004001756.1|        872
gi|426218478|ref|XM_004003425.1|        1143
gi|426218480|ref|XM_004003426.1|        2344
gi|426218482|ref|XM_004003427.1|        822
...

...

Did I make any errors?

Thanks a lot!

 

ADD REPLYlink written 4.3 years ago by Gerde0

If I can help you I have to see the codes you have before pwf=nullp(de.data,bias.data=gene.length).

ADD REPLYlink written 4.3 years ago by Parham1.4k
0
gravatar for Gerde
4.3 years ago by
Gerde0
China
Gerde0 wrote:

Hi Parham,

     The codes befor pwf-nullp() is as below:

library(goseq)
genes_list=read.table("gene.list",sep="\t")
de.data=as.integer(t(genes_list$V2))
names(de.data)=as.vector(t(genes_list$V1))
a=read.table("hs.fa.len",sep="\t")
gene.length<-as.vector(t(a$V2))
pwf=nullp(de.data, bias.data=gene.length)

 

ADD COMMENTlink written 4.3 years ago by Gerde0

Its not very clear to me what you are doing. One thing I can say is, do the bias.data and de.data have the same length?

ADD REPLYlink written 4.3 years ago by Parham1.4k

Could you please provide an example of :

  • genes_list
  • hs.fa.len?
ADD REPLYlink written 19 months ago by Ric220
0
gravatar for Gerde
4.3 years ago by
Gerde0
China
Gerde0 wrote:

Yes, no "NA" existed in dataframe "de.data", and length(de.data) == length(gene.length)

ADD COMMENTlink written 4.3 years ago by Gerde0
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