[BioC] Annotation problem with Microarray Gene Rat ST 1.0

[James W. MacDonald]

Hi Mrs. Kammermeier,

On 3/7/2013 4:29 AM, Antje Kammermeier wrote:
> Dear Members,
>
> I imported the CEL files with the ReadAffy() command. Using head() I got
> following error term:

This statement is completely vague. What type of celfiles? Using head() 
on what? When asking questions you need to be much more descriptive.

So if I put on my Carnack the Magnificent hat, I can divine several 
things. First, you used head() on the AffyBatch object you got from 
running ReadAffy() on your celfiles. In addition, you wanted to see the 
'head' of the values that were read in.

As you have found, you can't do this. If you just want to see numbers, 
you can use

head(exprs(celfiles))

if you want PM values

head(pm(celfiles))


>
> In x[seq_len(n)] :
>    The use of abatch[i,] and abatch[i] is deprecated. Please use abatch[,i]
> instead.
>
> Using the  command : mm(celfiles,'10700055')[1:3,]
> gives the NA in Mismatch data.
>
>            ControlW_D3.CEL ED_01_Kd5_09_10_28.CEL ED_02_Kd14_02_03_04.CEL
> 107000551              NA                     NA                      NA
> 107000552              NA                     NA                      NA
> 107000553              NA                     NA                      NA
>
> Is there any coincidence between these two commands. How can I convert the
> abatch[i] format into the abatch[,i] format.

I can further divine that you are using a random-primer based array (as 
compared to the 3'-biased arrays). In which case you should note that 
none of the random-primer based arrays have MM probes. If you had done

pm(celfiles,'10700055')[1:3,]

you would see some data.

Best,

Jim
>
>
> Thanks for your attention
>
> Mrs: Kammermeier
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099