Question: Problem in running NOISeq-sim
0
gravatar for jaspreetk.dhanjal
2.5 years ago by
jaspreetk.dhanjal10 wrote:

Hi,

I am using NOISeq-sim to analyze RNA-seq data with no replicates and find differentially expressed genes.

I created a count table containing read counts for one control and one cancer sample. Secondly I have a factors file defining the condition of two samples (one control and one cancer sample) with variables 'N' and 'T1' respectively.

Now, When i try to run the NOISeq-sim, I get an error saying- 'You must specify which conditions you wish to compare when the factor has two or more conditions.' However, my input files have only one control and one sample as mentioned above.

Kindly help!

#My code

library(NOISeq)

RawCountTable <- read.table("final-count.txt", header=TRUE, sep="\t", row.names=1)
SampleInfo <- read.table("design.csv", header=TRUE, sep=",")

N_T1 <- RawCountTable[SampleInfo$condition %in% c("N","T1")]
S <- subset(SampleInfo, condition %in% c("N","T1"))

myTMM = tmm(assayData(mydata)$exprs, long = 1000, lc = 0)
head(myTMM)
mydata_1 <- readData(data = myTMM, factors = S)
myresults <- noiseq(mydata_1, factor="condition", k = NULL, norm = "n", pnr = 0.2, nss = 5, v = 0.02, lc = 1, replicates = "no")

Error:

> myresults <- noiseq(mydata_1, factor="condition", k = NULL, norm = "n", pnr = 0.2, nss = 5, v = 0.02, lc = 1, replicates = "no")
[1] "Computing (M,D) values..."
Error in allMD(input, factor, k = k, replicates = replicates, norm = norm,  : 
  Error. You must specify which conditions you wish to compare when the factor has two or more conditions.
rna-seq tool noiseq • 1.3k views
ADD COMMENTlink modified 2.5 years ago by Benn8.1k • written 2.5 years ago by jaspreetk.dhanjal10

I have changed your post from "tool" to "question". The "tool" posts are meant for presenting new tools, questions about a tool should be marked as "question".

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Benn8.1k

Edit your question and post your code.

ADD REPLYlink written 2.5 years ago by h.mon32k

I am using NOISeq-sim to analyze RNA-seq data with no replicates and find differentially expressed genes.

Not what you are asking for, but you really should have replicates if you are doing differential expression analysis.

ADD REPLYlink written 2.5 years ago by WouterDeCoster45k

This module (NOISeq-sim) of NOISeq package has been developed to analyze the data with no technical or biological replicates.

I do have biological replicates (read counts from almost 1000 sample with same condition). But my objective is to study the differential expression for each sample individually, which will be used further for some other work. I don't want to use all the samples as biological replicates. I would really appreciate if you can suggest me some better way of doing the same.

Thanks!

ADD REPLYlink written 2.5 years ago by jaspreetk.dhanjal10

Hey, can you give the output of SampleInfo? Maybe there's an issue with that.

ADD REPLYlink written 19 months ago by Cookie-san110
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