[BioC] edgeR: error in readDGE

[Wolfgang Huber]

Dear Takuya

thanks, great.
The third file had apparently contained non-numeric values in the 
'COUNT' column, which you fixed subsequently.

	Wolfgang.


Il Nov/11/10 2:47 AM, $BB<ED(B $BBnLi(B ha scritto:
> Wolfgang,
>
> Thank you for your kind reply!
> I tried to change format by EXCEL (I am just beginner of R since this week...)
> Anyway it looks OK!
>
>
>
> BEFORE
>> for (f in targets$files)
> +  str(read.delim(f, stringsAsFactors=FALSE))
> 'data.frame':	42131 obs. of  2 variables:
>   $ SEQUENCE: chr  "AAACAGCAGAGAGAGAGAGAGAGAGAG" "AAACAGCAGGTACAAGATCTACCCGGG" "AAACAGCAGTGTTCTGAAGCCAAACTC" "AACAGCAGAAAAAGCTGCTGTCTCTGT" ...
>   $ COUNT   : int  0 0 0 0 0 0 0 0 0 0 ...
> 'data.frame':	42130 obs. of  2 variables:
>   $ AAACAGCAGAGAGAGAGAGAGAGAGAG: chr  "AAACAGCAGGTACAAGATCTACCCGGG" "AAACAGCAGTGTTCTGAAGCCAAACTC" "AACAGCAGAAAAAGCTGCTGTCTCTGT" "AACAGCAGAACAAGCTGCTGTCTCTGT" ...
>   $ X0                         : int  3 5 0 0 14 0 0 0 0 0 ...
> 'data.frame':	42131 obs. of  2 variables:
>   $ SEQUENCE: chr  "AAACAGCAGAGAGAGAGAGAGAGAGAG" "AAACAGCAGGTACAAGATCTACCCGGG" "AAACAGCAGTGTTCTGAAGCCAAACTC" "AACAGCAGAAAAAGCTGCTGTCTCTGT" ...
>   $ COUNT   : chr  "0" "0" "0" "0" ...
> 'data.frame':	42131 obs. of  2 variables:
>   $ SEQUENCE: chr  "AAACAGCAGAGAGAGAGAGAGAGAGAG" "AAACAGCAGGTACAAGATCTACCCGGG" "AAACAGCAGTGTTCTGAAGCCAAACTC" "AACAGCAGAAAAAGCTGCTGTCTCTGT" ...
>   $ COUNT   : int  0 0 0 0 0 0 0 0 0 0 ...
>
>
> AFTER
>
>> for (f in targets$files)
> +  str(read.delim(f, stringsAsFactors=FALSE))
> 'data.frame':	42131 obs. of  2 variables:
>   $ SEQUENCE: chr  "AAACAGCAGAGAGAGAGAGAGAGAGAG" "AAACAGCAGGTACAAGATCTACCCGGG" "AAACAGCAGTGTTCTGAAGCCAAACTC" "AACAGCAGAAAAAGCTGCTGTCTCTGT" ...
>   $ COUNT   : num  0 0 0 0 0 0 0 0 0 0 ...
> 'data.frame':	42131 obs. of  2 variables:
>   $ SEQUENCE: chr  "AAACAGCAGAGAGAGAGAGAGAGAGAG" "AAACAGCAGGTACAAGATCTACCCGGG" "AAACAGCAGTGTTCTGAAGCCAAACTC" "AACAGCAGAAAAAGCTGCTGTCTCTGT" ...
>   $ COUNT   : num  0 3 5 0 0 14 0 0 0 0 ...
> 'data.frame':	42131 obs. of  2 variables:
>   $ SEQUENCE: chr  "AAACAGCAGAGAGAGAGAGAGAGAGAG" "AAACAGCAGGTACAAGATCTACCCGGG" "AAACAGCAGTGTTCTGAAGCCAAACTC" "AACAGCAGAAAAAGCTGCTGTCTCTGT" ...
>   $ COUNT   : num  0 0 0 0 0 0 0 0 0 0 ...
> 'data.frame':	42131 obs. of  2 variables:
>   $ SEQUENCE: chr  "AAACAGCAGAGAGAGAGAGAGAGAGAG" "AAACAGCAGGTACAAGATCTACCCGGG" "AAACAGCAGTGTTCTGAAGCCAAACTC" "AACAGCAGAAAAAGCTGCTGTCTCTGT" ...
>   $ COUNT   : num  0 0 0 0 0 0 0 0 0 0 ...
>> d<- readDGE(targets)
>> d
> An object of class "DGEList"
> $samples
>      files group description lib.size norm.factors
> 1 GAT.txt    MT         FT9    65895            1
> 2 ACA.txt    WT         FT9    67888            1
> 3 ACT.txt    MT        FT10    65144            1
> 4 ACG.txt    WT        FT10    23938            1
>
> $counts
>                              1 2 3 4
> AAACAGCAGAGAGAGAGAGAGAGAGAG 0 0 0 0
> AAACAGCAGGTACAAGATCTACCCGGG 0 3 0 0
> AAACAGCAGTGTTCTGAAGCCAAACTC 0 5 0 0
> AACAGCAGAAAAAGCTGCTGTCTCTGT 0 0 0 0
> AACAGCAGAACAAGCTGCTGTCTCTGT 0 0 0 0
> 42126 more rows ...
>
>
> Thank you again.
>
> Best,
>
> Takuya
>
>
> On 2010/11/10, at 18:33, Wolfgang Huber wrote:
>
>> $BB<ED(B $BBnLi(B,
>>
>> It looks like the second column ("COUNT") in your files is not always numeric. Can you send the output of the following:
>>
>> for (f in targets$files)
>>   str(read.delim(f, stringsAsFactors=FALSE))
>>
>>
>> Best wishes
>> 	Wolfgang
>>
>> Il Nov/10/10 9:36 AM, $BB<ED(B $BBnLi(B ha scritto:
>>> I am a beginner of everything of R and edgeR; just like "copy and paste of the command" of the manual.
>>>
>>> I tried to make DGEList object like descriptions on page 9.
>>> I could make object, "target", as follows.
>>>> targets
>>>     files group description
>>> 1 GAT.txt    MT         FT9
>>> 2 ACA.txt    WT         FT9
>>> 3 ACT.txt    MT        FT10
>>> 4 ACG.txt    WT        FT10
>>>
>>> On the next command, I failed.
>>> d<- readDGE(targets)
>>>
>>> (I deleted "skip = 5, comment.char = "#"" from original command, because on my understanding,
>>> there were no rows to be skipped, nor comments.)
>>>
>>> error colSums(x$counts) :  'x' must be numeric
>>>
>>> This error message might be inaccurate, because it is localized.
>>>
>>> GAT.txt, and other txt files were made as a tab-delimited, plain-text, as follows, for example.
>>> SEQUENCE	COUNT
>>> AAACAGCAGAGAGAGAGAGAGAGAGAG	0
>>> AAACAGCAGGTACAAGATCTACCCGGG	0
>>> AAACAGCAGTGTTCTGAAGCCAAACTC	0
>>> ....
>>>
>>> I use R for Mac OSX GUI 1.35 and newest edgeR.
>>>
>>> I am very happy, if you have any comments.
>>> Thank you.
>>>
>>> Takuya
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>