Hi.
On Mon, Aug 23, 2010 at 11:14 AM, Gene <genetas...@gmail.com> wrote:
> I removed those plmData directories, but I still had the same error.
> I also tried running it on a computer with an older installation of
> aroma.affymetrix (since I have run this previously on this same data
> and it has worked), but with the same error. I do notice that it
> shows that all the fragment lengths are NA:
Yes, that seems to be the case. You must have got hold of an invalid
UFL file. Depending on which version of UFL file you get, you should
get something like this:
> ufl <- AromaUflFile$byChipType("Mapping250K_Sty");
> print(ufl);
AromaUflFile:
Name: Mapping250K_Sty
Tags: na26,HB20080916
Full name: Mapping250K_Sty,na26,HB20080916
Pathname: ../../../Documents/My Data/annotationData/chipTypes/Mapping250K_Sty/Ma
pping250K_Sty,na26,HB20080916.ufl
File size: 466.18 kB (477373 bytes)
RAM: 0.00 MB
Number of data rows: 238378
File format: v1
Dimensions: 238378x1
Column classes: integer
Number of bytes per column: 2
Footer: <platform>Affymetrix</platform><chipType>Mapping250K_Sty</chipType><crea
tedOn>20080916 17:13:53 PDT</createdOn><createdBy><fullname>Henrik Bengtsson</fu
llname><email>h...@stat.berkeley.edu</email></createdBy><srcFiles><srcFile1><filen
ame>Mapping250K_Sty.cdf</filename><filesize>184371335</filesize><checksum>8c7ffa
88bb444d953214f601bb998e51</checksum></srcFile1><srcFile2><filename>Mapping250K_
Sty.na26.annot.csv</filename><filesize>412941971</filesize><checksum>eb1ced7bd45
aa7c6f6edf9fb708c7441</checksum></srcFile2></srcFiles>
Chip type: Mapping250K_Sty
Platform: Affymetrix
> summary(ufl)
length
Min. : 115
1st Qu.: 440
Median : 598
Mean : 609
3rd Qu.: 771
Max. :1266
NA's : 681
If not, download the UFL file again from:
http://aroma-project.org/chipTypes/Mapping250K_Nsp-and-Mapping250K_Sty
/Henrik
>
> Finished reading CEL file.
> 20100823 11:06:13| Thetas:
> num [1:233566, 1] 971 811 1509 1323 486 ...
> 20100823 11:06:13| (Allele-specific) thetas:
> num [1:233566, 1] 971 811 1509 1323 486 ...
> 20100823 11:06:13| Total thetas:
> num [1:233566] 971 811 1509 1323 486 ...
> 20100823 11:06:13| Summary of total signals (on the intensity
> scale):
> Min. 1st Qu. Median Mean 3rd Qu. Max.
> 389 3780 5670 6700 8510 62600
> 20100823 11:06:14| Signals:
> num [1:233566] 9.92 9.66 10.56 10.37 8.93 ...
> 20100823 11:06:14| Summary of signals (on the log2 scale):
> Min. 1st Qu. Median Mean 3rd Qu. Max.
> 8.6 11.9 12.5 12.5 13.1 15.9
> 20100823 11:06:14| Fragment lengths:
> int [1:233566, 1] NA NA NA NA NA NA NA NA NA NA ...
> 20100823 11:06:14| Summary of fragment lengths:
> V1
> Min. : NA
> 1st Qu.: NA
> Median : NA
> Mean : NaN
> 3rd Qu.: NA
> Max. : NA
> NA's :233566
> 20100823 11:06:14| Fitting target prediction function to each enzyme
> exclusively...
> 20100823 11:06:14| Distribution of log2 signals that are finite:
> Mode TRUE NA's
> logical 233566 0
> 20100823 11:06:14| Distribution of units with known fragment
> lengths:
> V1
> Mode :logical
> FALSE:233566
> NA's :0
> 20100823 11:06:14| Enzyme #1 of 1...
> 20100823 11:06:14| Distribution of units with known fragment
> lengths and finite signals:
> Mode FALSE NA's
> logical 233566 0
> 20100823 11:06:14| Distribution of units with known fragment
> lengths and finite signals that are exclusively on this enzyme:
> Mode FALSE NA's
> logical 233566 0
> Error in list(`lapply(chipTypes, function(x) doCRMA("gsk", chipType =
> x, verbose = verbose` = <environment>, :
>
>
> Gene
>
> On Aug 19, 8:39 pm, Henrik Bengtsson <henrik.bengts...@gmail.com>
> wrote:
>> Hi Gene,
>>
>> did you add additional arrays to your rawData/ directory at anytime
>> after having ran the pipeline ones? If so, that would explain the
>> problem. The solution is then to delete the two plmData/
>> subdirectories:
>>
>> plmData/gsk,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/
>> plmData/gsk,ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY/Mapping250K_Sty/
>>
>> which we give you new probe-level model estimates. The thing is that
>> RmaCnPlm is a multi-array method, meaning that any estimates has to be
>> redone if you add new arrays. Since the fragment-length normalized
>> data depend on this too, you have to reestimate those as well. The
>> easiest way is to delete the corresponding plmData/ directories as
>> above.
>>
>> Hope this helps
>>
>> Henrik
>>
>> PS. Technically, you've detected a bug in RmaPlm, because it fails to
>> detect that new arrays have been added. Instead, it quietly pass
>> empty allocated chip-effect estimates to FragmentLengthNormalization
>> who has to deal with it ...and luckily detected it.
>>
>>
>>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
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>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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