Question

Microarray expression analysis

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manuchandwadkar • 0

@manuchandwadkar-22916

Last seen 4.7 years ago

Hello, I was doing normalization step in R but it is showing me this error..

>names=dir(pattern="CEL.gz")
> My_CELdata=ReadAffy(widget=TRUE)
Error: cannot allocate vector of size 2.6 Gb
> My_CELdata=ReadAffy(widget=TRUE)
Error: the following are not valid files:
    C:/users/bioproject1/Desktop/RAW_DATA$
> My_CELdata=ReadAffy(widget=TRUE)
Error in if (as.character(tkcurselection(selectView))[1] != "") { : 
  missing value where TRUE/FALSE needed
Error: cannot allocate vector of size 2.5 Gb

So how to proceed further now?

normalization • 645 views

ADD COMMENT • link updated 4.7 years ago by James W. MacDonald 67k • written 4.8 years ago by manuchandwadkar • 0

James W. MacDonald · Answer 1 · 2020-02-28

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 2 days ago

United States

If you get an error saying

Error: cannot allocate vector of size 2.5 Gb

That means you don't have enough RAM to do what you are trying to do.

Also, the Tcl/Tk stuff in affy has probably not been touched in like 15 years, so it might not really work any more? In addition, if the arrays are anything but old 3'-biased arrays (as ATpoint notes, you are being unnecessarily mysterious about what you are doing, so we are left guessing) then you shouldn't be using affy, but instead you should use oligo, which doesn't have the wiget interface.

So, you need to

Get a computer with more RAM
Alternatively try justRMA which is memory efficient
Do a better job of describing what you are trying to do, what arrays you have, how many, how much RAM you have, what OS, etc

ADD COMMENT • link 4.8 years ago James W. MacDonald 67k

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t<-expresso(My_CEL,normalize.method="qspline",bgcorrect.method="mas",pmcorrect.method="pmonly",summary.method="mas")
background correction: mas 
normalization: qspline 
PM/MM correction : pmonly 
expression values: mas 
background correcting...Error: cannot allocate vector of size 1.0 Gb

what to do now?

ADD REPLY • link updated 4.7 years ago by James W. MacDonald 67k • written 4.7 years ago by manuchandwadkar • 0

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Warning message:
In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Program Files\R\R-3.6.2\library\00LOCK\digest\libs\i386\digest.dll to C:\Program Files\R\R-3.6.2\library\digest\libs\i386\digest.dll: Permission denied

what should i do now?

ADD REPLY • link updated 4.7 years ago by James W. MacDonald 67k • written 4.7 years ago by manuchandwadkar • 0

score 0 · Answer 2 · 2020-03-02

Three things:

When you post code, either put a triple backtick (the upper left key on a QWERTY keyboard) on the line before your code, and the line after, or highlight and click the box that has 10101010 in it.
I advised you to try justRMA, saying it is more memory efficient, but instead you tried expresso, which is not. And then you got another message saying you don't have enough RAM. Seems pretty clear what the problem is, no? You ignored my advice and now are asking for more. Seems prudent to try what I recommended first, but ymmv.
Just showing a warning message without any code that preceded it isn't helpful. You have to remember that nobody else knows what you are doing, what you did, how your system is set up, etc. It so happens that I have been doing this long enough to know that on Windows 7 and later, making changes to C:\Program Files requires administrator privileges and R doesn't (normally) run with that level of privileges, so cannot make changes to packages in that directory. Ideally you wouldn't have your library dir in a protected place like that, and a well crafted Google search should help you to change your situation.