Thank you so much. I will try this as soon as I can.
On 2013-11-17 10:23 PM, "Martin Morgan" <mtmorgan@fhcrc.org> wrote:

> On 11/17/2013 12:11 PM, Jobin K. Varughese wrote:
>
>> Hello again. I was informed that I should share this as a public Dropbox
>> link rather than as an attachment. This link can be found here:
>> https://dl.dropboxusercontent.com/u/6322354/ExpressionSet_error.zip
>>
>
> Hi Jobin -- I installed and loaded the package then
>
>   debug(loadReadCounts)
>   source("stats.R")
>
> and then stepped through the function until I got to
>
>         res <- new("shrnaSet", assayData=adata, phenoData=pdata,
> featureData=fdata)
>
> when I ran this I got the error
>
> Browse[2]> new("shrnaSet", assayData=adata, phenoData=pdata,
> featureData=fdata)
> Error in validObject(.Object) :
>   invalid class "shrnaSet" object: featureNames differ between assayData
> and featureData
>
> so I looked at the rownames of the objects inside adata, and the rownames
> of fdata, which are supposed to be the same
>
> Browse[2]> eapply(adata, function(x) head(rownames(x)))
> $readCounts1
> [1] "X4501844.NM_001088.1.38903" "X4501844.NM_001088.1.38904"
> [3] "X4501844.NM_001088.1.38905" "X4501844.NM_001088.1.38906"
> [5] "X4501844.NM_001088.1.38907" "X4501844.NM_001088.1.54352"
>
> $readCounts2
> [1] "X4501844.NM_001088.1.38903" "X4501844.NM_001088.1.38904"
> [3] "X4501844.NM_001088.1.38905" "X4501844.NM_001088.1.38906"
> [5] "X4501844.NM_001088.1.38907" "X4501844.NM_001088.1.54352"
>
> Browse[2]> head(rownames(pData(fdata)))
> [1] "4501844|NM_001088.1|38903" "4501844|NM_001088.1|38904"
> [3] "4501844|NM_001088.1|38905" "4501844|NM_001088.1|38906"
> [5] "4501844|NM_001088.1|38907" "4501844|NM_001088.1|54352"
>
> They're not the same, because earlier in the code the package author had
> made the names of the assay data with 'make.names'
>
>     x <- read.delim(file=paste(dataPath,condition2,sep="/"), header=TRUE)
>     condition2 <- as.matrix(x[,2:dim(x)[2]])
>     rownames(condition2) <- make.names(x[,1],unique=TRUE)
>
> but the names of the feature data were not mangled
>
>     fdat = read.delim(file=paste(dataPath,shRNAData,sep="/"), header=TRUE)
>     rownames(fdat) <- fdat[,1]
>
> I guess a work-around would be to mangle the names of the first column of
> shRNALibrary.txt using make.names(). I think I would have written the code
> above without mangling names as
>
>     condition2 = as.matrix(read.delim(file.path(dataPath, condition2),
> header=TRUE, row.names=1))
>
> and (with similar changes elsewhere in this code)
>
>     fdat = read.delim(file.path(dataPath,shRNAData), header=TRUE,
> row.names=1)
>
> Martin
>
>
>> Thank you.
>>
>> Jobin
>>
>>
>> On Sat, Nov 16, 2013 at 1:25 PM, Jobin K. Varughese <jobinv@gmail.com
>> >wrote:
>>
>>  Hello. My name is Jobin K. Varughese MD PhD, and I work at the University
>>> of Bergen, Norway.
>>>
>>> My issue is that I am having trouble with the ExpressionSet class. It
>>> appears when running the following command (adapted from the shRNAseq<
>>> http://rock.icr.ac.uk/software/shrnaseq.jsp>vignette):
>>>
>>>  library(shRNAseq)
>>>> dataPath <- ".."
>>>>
>>>> x <- loadReadCounts(
>>>>
>>> +   screenData="phenoData.txt",
>>> +   shRNAData="shRNALibrary.txt",
>>> +   condition1="raw_tmz.txt", condition1Name="TMZ",
>>> +   condition2="raw_ctrl.txt", condition2Name="Control",
>>> +   dataPath=dataPath)
>>>
>>> Error in validObject(.Object) :
>>>    invalid class “shrnaSet” object: featureNames differ between
>>> assayData and featureData
>>>
>>> I've made sure that the featureNames are indeed identical between the
>>> various files. Next, I tried contacting the developer of shRNAseq and
>>> even
>>> sent him my raw data files. He attempted several strategies to solve the
>>> issue: *"I've changed the names in the first columns to numbers 1:27500
>>> and made sure they match exactly between the files - didn't help. I've
>>> checked line endings (Mac/Unix/Windows) - didn't help. I've removed the
>>> final blank lines - didn't help. I've stripped quotes - didn't help."*
>>>
>>> Eventually he also was unable to get past the error message, but could
>>> provide the following: *"The shRNAset object is basically an expression
>>> set (Eset) and the methods are inherited from that (including the error
>>> message)."*
>>>
>>> The error is reproducible with the sample files that I've attached
>>> (compressed with 7zip). I have also attached the output from
>>> sessionInfo()
>>> and traceback().
>>>
>>> Can anyone advise me as to what might be the problem? I would be very
>>> grateful indeed.
>>>
>>> Sincerely,
>>> Jobin K. Varughese
>>>
>>>
>>         [[alternative HTML version deleted]]
>>
>>
>>
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>>
>
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