Dear Sara, We think there is no problem at all with your data. You can keep on doing your analysis following the manual and we don't expect you to have any kind of problem. You got an error message because you are applying the head() function to the object generated by readData(). You do not have to do that with this kind of objects. Just type the name of the object and a little summary will be shown. We appreciate your interest and we will fix NOISeq as soon as possible so it does not return this error message anymore. Best regards, Sonia Tarazona On 10/11/2012 07:19 PM, Dan Tenenbaum wrote: > I'm CC'ing the maintainer of the NOISeq package who may be able to > answer your question. > Dan > > > On Thu, Oct 11, 2012 at 1:32 AM, sara wilson [guest] > <guest at="" bioconductor.org=""> wrote: >> Hi and good day, >> >> I am totally new to R so sorry is my question is so naive. >> I am just following the NOISeq tutorial with my own data set.Below is what I have in order to make the readData: >> >> my data: >>> head(counts) >> V2 V3 V4 V5 V6 V7 V8 V9 >> 1/2-SBSRNA4 3 5 4 4 2 3 1 1 >> A1BG 200 93 246 102 86 46 58 85 >> A1BG-AS1 24 28 16 32 17 10 19 14 >> A1CF 1 1 1 2 1 0 0 1 >> A2LD1 100 71 98 97 59 128 88 114 >> A2M 5 5 23 1 5 6 10 5 >> >>> class(counts) >> [1] "data.frame" >> >> my factors : >>> factors >> sex >> 1 Female >> 2 Female >> 3 Female >> 4 Female >> 5 Male >> 6 Male >> 7 Male >> 8 Male >> >> and my length : >>> head(mylength) >> 1/2-SBSRNA4 A1BG A1BG-AS1 A1CF A2LD1 A2M >> 23 916 160 7 755 60 >>> class(mylength) >> [1] "integer" >> >> when I run the command readData, without the length property it produces the object but with the length property, there is an error. so there should be problem with that but I do not know what is it. >> Many thanks in advance. >> >> -- output of sessionInfo(): >> >>> noy1 <- readData(data=counts, factors=factors, length= mylength) >>> head(noy1) >> Error in value[[3L]](cond) : invalid 'row.names' length >> AnnotatedDataFrame 'initialize' could not update varMetadata: >> perhaps pData and varMetadata are inconsistent? >> >> and then without length: >> >>> noy1 <- readData(data=counts, factors=factors) >>> head(noy1) >> ExpressionSet (storageMode: lockedEnvironment) >> assayData: 1 features, 8 samples >> element names: exprs >> protocolData: none >> phenoData >> sampleNames: V2 V3 ... V9 (8 total) >> varLabels: sex >> varMetadata: labelDescription >> featureData: none >> experimentData: use 'experimentData(object) >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Sonia Tarazona PhD Student Bioinformatics & Genomics Department Centro de Investigaci?n Pr?ncipe Felipe http://bioinfo.cipf.es