Hi Heyi,

The read quality tells us about the quality of each short read in the
general sense of
 "sum of quality scores over one short read" / "width of the short
read".   The
density is a measurement of the dispersed mass of the distribution of
the input.
The input to the density calculation is the normalized quality score I
mention above. 
See ?density for information on the algorithms used and why the length
of the
readQualityScore dataframe is 512.

What version of R and ShortRead are you using? It is helpful if you
provide this information
by calling sessionInfo() at the end of your code when submitting a question.

In R-devel (2.12) with ShortRead 1.7.24 this piece of code woks for me.
Please
let me know if you can run it.

# perform qa on a fastq file provided with ShortRead
exptPath <- system.file("extdata", package = "ShortRead")
sp <- SolexaPath(exptPath)
res <- qa(dirPath=analysisPath(sp), pattern="s_1_sequence.txt",
type="fastq")

> res
class: FastqQA(9)
QA elements (access with qa[["elt"]]):
  readCounts: data.frame(1 3)
  baseCalls: data.frame(1 5)
  readQualityScore: data.frame(512 4)
  baseQuality: data.frame(94 3)
  alignQuality: data.frame(1 3)
  frequentSequences: data.frame(50 4)
  sequenceDistribution: data.frame(3 4)
  perCycle: list(2)
    baseCall: data.frame(141 4)
    quality: data.frame(341 5)
  perTile: list(2)
    readCounts: data.frame(0 4)
    medianReadQualityScore: data.frame(0 4)


> report(res)
[1] "/tmp/RtmpCq1M5h/file8edbdab/index.html"

 
Valerie



On 09/24/2010 01:04 PM, heyi xiao wrote:
>
>
>
> Dear
> Martin,
>
> I used
> the qa function ShortRead package for the solexa sequencing data quality assessment.
> And I got some result in a FastqQA object below. 
>
>   
>>     
> qa1
>
> class:
> FastqQA(9)
>
> QA
> elements (access with qa[["elt"]]):
>
> Ā  readCounts: data.frame(1 3)
>
> Ā  baseCalls: data.frame(1 5)
>
> Ā  readQualityScore: data.frame(512 4)
>
> Ā  baseQuality: data.frame(94 3)
>
> Ā  alignQuality: data.frame(1 3)
>
> Ā  frequentSequences: data.frame(50 4)
>
> Ā  sequenceDistribution: data.frame(5 4)
>
> Ā  perCycle: list(2)
>
> Ā Ā Ā  baseCall: data.frame(157 4)
>
> Ā Ā Ā  quality: data.frame(1070 5)
>
> Ā  perTile: list(2)
>
> Ā Ā Ā  readCounts: data.frame(0 4)
>
> medianReadQualityScore: data.frame(0 4)
>
> Ā 
>
> But
> a few things are not that clear to me. What is readQualityScore, and what are
> the quality and density columns in it? I have 1000 reads in my example file,
> but there are only 512 rows. I try to generated report as suggested by the
> vignette, but failed in the follow ways:
>
> Ā 
>
>   
>>     
> rpt <- report(qa1)Ā Ā Ā Ā Ā  # Create
> report 
>
> Error
> in X11(paste("jpeg::", quality, ":", filename, sep =
> ""), width,Ā  : 
>
> Ā  unable to start device JPEG
>
> In
> addition: Warning message:
>
> In
> jpeg(file.path(imgDir, jpegFile), ...) :
>
> Ā  no jpeg support in this version of R
>
>   
>>     
> rpt <- report(qa1, type='pdf')Ā Ā Ā Ā Ā  #
> Create report 
>
> Error:
> UserArgumentMismatch
>
> Ā  'report, type="pdf"' not
> implemented for class 'FastqQA'
>
> Ā 
>
> I
> am working on a Lunix server remotely, I donāEUR^(TM)t really have X11 access.
> Unfortunately, the pdf method is not supported somehow. Is there any way that I
> can still generate the report?
>
> Heyi
>
>
>
>
>       
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>
>   
>
>
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