Question: Agilent microrna microaaray
0
gravatar for arisarkar88
24 months ago by
arisarkar880 wrote:

Hello,

          How to analyze data corresponding to Agilent-019118 Human miRNA Microarray 2.0 G4470B? I am bit stuck with this.

ADD COMMENTlink modified 24 months ago • written 24 months ago by arisarkar880

This question is unanswerable as asked. It's like asking 'How do I drive a car?', and the answer is 'Uh, by getting in and driving it?'.

If you have a specific question, and have some code that you have tried, then maybe somebody could help you. But asking non-specific, open-ended questions won't generate much enthusiasm to help you.

ADD REPLYlink written 24 months ago by James W. MacDonald50k
Answer: Agilent microrna microaaray
0
gravatar for arisarkar88
24 months ago by
arisarkar880 wrote:

Sorry..I should have posted the exact error. This was really non-specific. Thank you for pointing out this. The error was:

In read.table(file = file, header = header, sep = sep, quote = quote,  :
  incomplete final line found by readTableHeader on ...

<font face="monospace">I was using readTargets to read the array files and there was no incomplete final line. Please suggest how to proceed.</font>

ADD COMMENTlink written 24 months ago by arisarkar880

Please don't answer your own question with a comment (the box below, labeled 'Add your answer' is for adding answers, not additional comments. Use 'ADD COMMENT' for that).

Your question has nothing to do with any Bioconductor packages, and instead is a basic question about importing data into R. You could just google that error to get (does a quick google search) 3,930 responses to people asking about that exact error message. That's what you should almost always do first. Learning to help yourself will get you farther faster than asking people on a message board.

In future, you should post questions about basic R stuff to r-help@r-project.org, but AFTER you have tried googling for solutions.

That said, are you trying to read an Excel worksheet? You can't use read.table to read an XML document - you need one of the CRAN packages designed for that, like openxlsx etc.

> read.table("Book1.xlsx")
              V1
1 PK\003\004\024
Warning messages:
1: In read.table("Book1.xlsx") : line 1 appears to contain embedded nulls
2: In read.table("Book1.xlsx") :
  incomplete final line found by readTableHeader on 'Book1.xlsx'

 

ADD REPLYlink written 24 months ago by James W. MacDonald50k

I am well aware that the reply should be posted in 'ADD COMMENT' instead of 'ADD ANSWER' which I have followed through all my previous posts. Unfortunately, this time I was working on a desktop which suddenly had some problem and the reply was posted in 'ADD ANSWER' instead of  'ADD COMMENT'. I tried to rectify it but there was no option. Really sorry for that.

Besides, I know it is much easier to surf through google and get an answer which I have already done for this error and tried all possible solutions. It was only after all those trials that I thought of posting my query herein (hoping to get some help!!!).

I was trying to read the array files using readTargets and was not using .xlsx (which is obviously not possible in this case)

> library("limma", lib.loc="~/R/win-library/3.3")

> targets=readTargets()

Targets.txt had the following entries:

FileName Condition

GSM1079562_neuron_1.txt con

GSM1079563_neuron_2.txt con

GSM412071_nb_1.txt test

GSM412072_nb_2.txt test

Hope this helps.

ADD REPLYlink written 24 months ago by arisarkar880
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