[BioC] reading imagene files with LIMMA]

[smohapat at vbi.vt.edu]

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
>>>
>>>
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>>>
>> <smohapat.vcf>
>>
>