[BioC] reading imagene files with LIMMA

[Yi Xing]

Here is my sessionInfo()

 > sessionInfo()
R version 2.1.1, 2005-06-20, powerpc-apple-darwin7.9.0

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     
"datasets"
[7] "base"

other attached packages:
   limma
"2.0.8"


Thanks for your suggestion. I'll upgrade my packages.
On Jun 28, 2007, at 3:39 PM, smohapat at vbi.vt.edu wrote:

> Yi:
>
> Could you send the output of sessionInfo() to the list? I am attaching
> mine at the end.
>
> I guess that you are using an old version of limma (when field 
> dimensions
> had only one block). It is recommended to upgrade to a more recent 
> version
> (e.g., 2.10.5).
>
>> so read.imagene() calculates the total number of spots as prod(FD):
>> nspots <- prod(FD) Y <- matrix(0, nspots, narrays)
>
> Looking at the actual code of read.imagene gives
> nspots <- sum(apply(FD, 1, prod))
>
> which seems good enough to handle your situation.
>
> Best,
>
> Saroj
>
> -------------------------------
>> sessionInfo()
> R version 2.5.0 (2007-04-23)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  
> "methods"
> [7] "base"
>
> other attached packages:
>    limma
> "2.10.5"
> --------------------------------
>
>
>
>>
>
>
>
> On Thu, June 28, 2007 5:33 pm, Yi Xing wrote:
>> Hello Saroj,
>>
>>
>> Thanks for your message. I think the problem is with the Field
>> Dimensions. It looks like this for my file:
>>
>>
>> Field     Metarows Metacols Rows Cols
>> Block1         1        1   15   14
>> Block2         1        1   15   14
>> Block3         1        1   15   14
>> Block4         1        1   15   14
>> Block5         1        1   15   14
>> Block6         1        1   15   14
>> Block7         1        1   15   14
>> Block8         1        1   15   14
>> Block9         1        1   15   14
>> Block10        1        1   15   14
>> Block11        1        1   15   14
>> Block12        1        1   15   14
>> Block13        1        1   15   14
>> Block14        1        1   15   14
>> Block15        1        1   15   14
>> Block16        1        1   15   14
>> Block17        1        1   15   14
>> Block18        1        1   15   14
>> Block19        1        1   15   14
>> Block20        1        1   15   14
>> Block21        1        1   15   14
>> Block22        1        1   15   14
>> Block23        1        1   15   14
>> Block24        1        1   15   14
>> Block25        1        1   15   14
>> Block26        1        1   15   14
>> Block27        1        1   15   14
>> Block28        1        1   15   14
>> Block29        1        1   15   14
>> Block30        1        1   15   14
>> Block31        1        1   15   14
>> Block32        1        1   15   14
>>
>>
>>
>> which is 2.046527e+74, causing the error in the next line.
>>
>> Yi
>> On Jun 28, 2007, at 2:21 PM, Saroj Mohapatra wrote:
>>
>>
>>> Hello Yi,
>>>
>>>
>>> It is possible that there is a discrepancy between the number of 
>>> spots
>>> calculated from the Field Dimensions in header and the number of 
>>> rows it
>>> actually reads from the file.
>>>
>>> For example, in my Imagene 5.1 file:
>>> in the header, below "Begin Field Dimensions" I find the following:
>>> Metarows = 8
>>> Metacols = 4
>>> Rows = 15
>>> Cols = 12
>>>
>>>
>>> So, the total number of spots = 5760
>>> In the data section of my file, there are 5760 rows (excluding column
>>> titles).
>>>
>>> Of course, the actual number would vary, you would have a different
>>> number of spots. You could start with checking that the numbers 
>>> match.
>>>
>>> Also, there should be something like "Begin Raw Data" before the 
>>> first
>>> line and "End Raw Data" after the last line of data section.
>>>
>>> Good luck!
>>>
>>>
>>> Saroj
>>>
>>>
>>> Yi Xing wrote:
>>>
>>>
>>>> Hi,
>>>>
>>>>
>>>> I tried to read several Imagene files with LIMMA:
>>>>
>>>>
>>>> library(limma) targets<-readTargets()
>>>> files<-targets[,c("FileNameCy3","FileNameCy5")]
>>>> RG<-read.maimages(files,source='imagene')
>>>>
>>>>
>>>> however, I got this error message:
>>>>
>>>> Read header information
>>>> Error in matrix(0, nspots, narrays) : matrix: invalid 'nrow' value
>>>> (too large or NA)
>>>> In addition: Warning message:
>>>> NAs introduced by coercion
>>>>
>>>>
>>>> What might be the problem and how to fix it? Thanks.
>>>>
>>>>
>>>> Yi Xing
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>>
>>> <smohapat.vcf>
>>>
>>
>
>