Question

Error in E-Eb Limma package

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diego.orihuelatacuri • 0

@diegoorihuelatacuri-22214

Last seen 5.2 years ago

Instituto Nacional de Salud del Niño, L…

Hello!

I have load my RGList in Limma to start analysis but when I want to apply some functions (for example: plotMA3by2) R shows the error: "Error in E - Eb : non-numeric argument to binary operator".

*Code:

RG <- read.maimages(targets,source="generic",columns=list(R="R_Raw_intensity_mean",
G="G_Raw_intensity_mean",Rb="R_Background_mean",Gb="G_Background_mean"),
annotation=c("Num","meta_row","meta_col","row1","col","Oligo_ID","Gene_symbol",
"Gene_ID","Transcript_ID"),sep=" ")
plotMA3by2(RG, prefix="MA", main=colnames(object),
           zero.weights=FALSE, common.lim=TRUE, device="png")

How could I fix this error?

Please, help me...

Thank you!!

limma error E-Eb • 982 views

ADD COMMENT • link updated 5.2 years ago by Gordon Smyth 52k • written 5.2 years ago by diego.orihuelatacuri • 0

Gordon Smyth · Answer 1 · 2019-10-24

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Gordon Smyth 52k

@gordon-smyth

Last seen 40 minutes ago

WEHI, Melbourne, Australia

I am pretty sure that the error message you state is not actually possible from the code shown in your question. The operation E-Eb is only relevant for EList objects, not RGList objects, and the operation E-Eb does not appear in the plotMA3by2 function anyway.

I am guessing that you might be running other lines of code that are not shown here.

Did you get messages from the read.maimages step? As far as trouble shooting is concerned, you might try by typing

class(RG
names(RG)
lapply(RG, class)
show(RG)

ADD COMMENT • link 5.2 years ago Gordon Smyth 52k

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Hello Gordon,

Thank you so much for your answer. I know the operation E-Eb is for EList object. When I check the class it indicates that is a RGList.

I typed the code you gave me and this is the response:

> class(RG)
[1] "RGList"
attr(,"package")
[1] "limma"
>       names(RG)
[1] "R"       "G"       "Rb"      "Gb"      "targets" "genes"   "source" 
>       lapply(RG, class)
$R
[1] "matrix"

$G
[1] "matrix"

$Rb
[1] "matrix"

$Gb
[1] "matrix"

$targets
[1] "data.frame"

$genes
[1] "data.frame"

$source
[1] "character"

>       show(RG)
An object of class "RGList"
$R
     dmel-13       dmel-14      dmel-15       dmel-16       dmel-19       dmel-20      
[1,] "840,711538"  "663,230769" "938"         "935,596154"  "756,903846"  "924,653846" 
[2,] "846,538462"  "664"        "1033,038462" "926,057692"  "782,807692"  "992,923077" 
[3,] "638,038462"  "349,557692" "649,576923"  "517,192308"  "407,019231"  "579,230769" 
[4,] "593,25"      "338,75"     "638,115385"  "514,134615"  "398,019231"  "651,115385" 
[5,] "1489,365385" "971,865385" "1458,076923" "1548,019231" "1681,923077" "1734,942308"
29947 more rows ...

$G
     dmel-13      dmel-14      dmel-15      dmel-16      dmel-19       dmel-20     
[1,] "158,519231" "215,903846" "184,923077" "274,038462" "278,730769"  "222,192308"
[2,] "167,538462" "249,365385" "260"        "319,942308" "381,230769"  "310,730769"
[3,] "133,173077" "156,692308" "149,384615" "135,538462" "156,461538"  "113,461538"
[4,] "126,134615" "143,25"     "145,134615" "135,75"     "153,423077"  "120,134615"
[5,] "716,826923" "607,096154" "699,346154" "943,519231" "1291,076923" "932,538462"
29947 more rows ...

$Rb
     dmel-13     dmel-14     dmel-15      dmel-16     dmel-19     dmel-20    
[1,] "78,316327" "50,622449" "97,153061"  "92,540816" "57,428571" "76,806122"
[2,] "84,020408" "50,5"      "107,05102"  "86,061224" "57,193878" "73,908163"
[3,] "95,408163" "50,530612" "122,857143" "78,336735" "54,989796" "69,316327"
[4,] "86,377551" "48,418367" "119,367347" "88,030612" "55,693878" "74,336735"
[5,] "80,806122" "49,173469" "148,877551" "94,163265" "57,908163" "72,091837"
29947 more rows ...

$Gb
     dmel-13     dmel-14      dmel-15      dmel-16     dmel-19      dmel-20    
[1,] "71,673469" "108,989796" "107,44898"  "94,112245" "101,489796" "78,755102"
[2,] "73,214286" "110,285714" "106,785714" "92,459184" "100,520408" "76,22449" 
[3,] "73,918367" "107,418367" "108,214286" "92,744898" "96,459184"  "74,979592"
[4,] "76,010204" "106,255102" "107,408163" "90,306122" "95,816327"  "76,683673"
[5,] "74,153061" "103,55102"  "109,285714" "87,469388" "102,336735" "78,540816"
29947 more rows ...

$targets
        SlideNumber    FileName     Cy3     Cy5      Date
dmel-13          13 dmel-13.txt control  microg 2019/9/27
dmel-14          14 dmel-14.txt  microg control 2019/9/27
dmel-15          15 dmel-15.txt control  microg 2019/9/27
dmel-16          16 dmel-16.txt  microg control 2019/9/27
dmel-19          19 dmel-19.txt control  microg 2019/9/27
dmel-20          20 dmel-20.txt  microg control 2019/9/27

$genes
  Num meta_row meta_col row1 col   Oligo_ID Gene_symbol Gene_ID Transcript_ID
1   1        1        1    1   1 DM00000828     CG12155 CG12155    CG12155-RA
2   2        1        1    1   2 DM00000828     CG12155 CG12155    CG12155-RA
3   3        1        1    1   3 DM00000809        Adam CG12131    CG12131-RA
4   4        1        1    1   4 DM00000809        Adam CG12131    CG12131-RA
5   5        1        1    1   5 DM00000802     CG12124 CG12124    CG12124-RA
29947 more rows ...

$source
[1] "generic"

Do you see some mistake?

I've been thinking about a possible error in the files I edited... Could be possible??

Thank you!!!

ADD REPLY • link updated 5.2 years ago by Gordon Smyth 52k • written 5.2 years ago by diego.orihuelatacuri • 0

0

Entering edit mode

Yes, the problem is obvious from the output. All the entries for R, G, Rb and Gb are character strings instead of numbers.

Is it possible that your original data file is using commas to indicate decimal points (i.e., using continental Europe style) but using a standard version of R that assumes dots for decimal points.

ADD REPLY • link 5.2 years ago Gordon Smyth 52k