Question: Problem in running NOISeq-sim
0
gravatar for jaspreetk.dhanjal
14 months ago by
jaspreetk.dhanjal0 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 • 575 views
ADD COMMENTlink modified 14 months ago by Benn7.8k • written 14 months ago by jaspreetk.dhanjal0

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 14 months ago • written 14 months ago by Benn7.8k

Edit your question and post your code.

ADD REPLYlink written 14 months ago by h.mon27k

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 14 months ago by WouterDeCoster41k

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 14 months ago by jaspreetk.dhanjal0

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

ADD REPLYlink written 3 months ago by Cookie-san40
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