Hi Pedro,

Thanks for the reply. I understand what you mean. 
I was able to solve the issue of reading the data 
and cvArray function by going through your 
replies in the mailing list. The problem I am 
having now is with the FilterMicroRna function. 
It doesn't matter how I read the data (either 
with read.maimages or AgiMicroRnaAFE), the 
filtering function is giving error messages.

Here is the session info:
 >  library("AgiMicroRna")
 >  targets.micro=readTargets(infile="targets.txt", verbose=TRUE)
 > 
ddaux=read.maimages(files=targets.micro$FileName,source="agilent", 
other.columns=list(IsGeneDetected="gIsGeneDetected", 
IsSaturated="gIsSaturated", 
IsFeatNonUnifOF="gIsFeatNonUnifOL", 
IsFeatPopnOL="gIsFeatPopnOL", 
ChrCoord="chr_coord", BGKmd="gBGMedianSignal", 
BGKus="gBGUsed"), 
columns=list(Rf="gTotalGeneSignal", 
Gf="gTotalProbeSignal", 
Rb="gMeanSignal",Gb="gProcessedSignal"), verbose=TRUE,sep="\t",quote="")
Read 36_DMSO_1.txt
Read 36_DMSO_2.txt
Read 36_DMSO_3.txt
Read 36_TCDD_1.txt
Read 36_TCDD_2.txt
Read 36_TCDD_3.txt
Read 60_DMSO_1.txt
Read 60_DMSO_2.txt
Read 60_DMSO_3.txt
Read 60_TCDD_1.txt
Read 60_TCDD_2.txt
Read 60_TCDD_3.txt
 > names(ddaux)
[1] "R"       "G"       "Rb"      "Gb"      "targets" "genes"   "source"
[8] "other"
 > names(ddaux$genes)
  [1] "Row"            "Col"            "Start"          "Sequence"
  [5] "ProbeUID"       "ControlType"    "ProbeName"      "GeneName"
  [9] "SystematicName" "Description"
 > ddaux$genes=ddaux$genes[,c(6,7,8)]
 > cvArray(ddaux, "MeanSignal", targets.micro, verbose=TRUE)
Foreground: MeanSignal

         FILTERING BY ControlType FLAG

  RAW DATA:                       5335
  PROBES without CONTROLS:        4620
----------------------------------
   (Non-CTRL) Unique Probe:  490
   (Non-CTRL) Unique Genes:  231
----------------------------------
DISTRIBUTION OF REPLICATED NonControl Probes
reps
   5   6   7  10
  20  18  36 416
------------------------------------------------------
Replication at Probe level- MEDIAN  CV
36_DMSO_1 36_DMSO_2 36_DMSO_3 36_TCDD_1 36_TCDD_2 
36_TCDD_3 60_DMSO_1 60_DMSO_2
     0.078     0.081     0.091     0.081 
0.077     0.067     0.076     0.066
60_DMSO_3 60_TCDD_1 60_TCDD_2 60_TCDD_3
     0.103     0.073     0.086     0.069
------------------------------------------------------
DISTRIBUTION OF REPLICATED Noncontrol Genes
reps
  20
231
------------------------------------------------------
 > ddTGS.rma = rmaMicroRna(ddaux, normalize=TRUE, background=FALSE)
Calculating Expression
 > ddPROC = filterMicroRna(ddTGS.rma, ddaux, 
control = TRUE, IsGeneDetected = TRUE, 
wellaboveNEG = FALSE, limIsGeneDetected = 50, 
limNEG = 25, makePLOT = FALSE, targets.micro, verbose = TRUE)
FILTERING PROBES BY FLAGS


FILTERING BY ControlType
Error in data.frame(as.character(PROBE_ID), 
as.character(GENE_ID), as.character(probe.chr),  :
   arguments imply differing number of rows: 231, 0




At 02:21 AM 6/16/2010, Pedro López Romero wrote:
>Hi,
>
>I don´t understand why you are using 
>ddaux=read.maimages and  then 
>dd=readMicroRnaAFE(targets.micro, verbose=TRUE). 
>If readMicroRnaAFE is giving you a problem with 
>the selection of the columns (this function 
>selects dd$genes=ddaux$genes[,c(4,5,6)], that 
>should correspond to "ControlType" "ProbeName" 
>and  "GeneName"), and you are using 
>ddaux=read.maimages don´t use the readMicroRnaAFE at all.
>
>Try ddaux=read.maimages(...) and then use this 
>ddaux object in your next calls to the 
>functions, making first the selection of columns 
>you want to do. What you are doing I guess is 
>right, but change 
>"dd$genes=ddaux$genes[,c(6,7,8)]" by "ddaux$genes=ddaux$genes[,c(6,7,8)]"
>
>ddaux=read.maimages(...)
>ddaux$genes=ddaux$genes[,c(6,7,8)].
>
>HTH
>
>p.-
>
>
>-----Mensaje original-----
>De: Neel Aluru [mailto:naluru@whoi.edu]
>Enviado el: Monday, June 14, 2010 10:37 PM
>Para: Pedro López Romero
>CC: bioc
>Asunto: Re: [BioC] AgiMicroRna - FilterMicroRna question
>
>Hi Pedro,
>
>I tried following your suggestions and I still 
>an error message as, "FILTERING BY ControlType
>Error in data.frame(as.character(PROBE_ID), 
>as.character(GENE_ID), 
>as.character(probe.chr),  :  arguments imply differing number of rows: 231, 0".
>
>I looked into the mailing list archive and I saw 
>one post there with similar issue but they were 
>trying to modify the source code. I am not an 
>expert in R and do not want to play with source code.
>
>If you have any suggestions on where the problem 
>lies with the above error message, that will be 
>great. Sorry to bother you on this.
>
>Thank you very much for your help.
>
>Sincerely, Neel
>
>  The following is the session info.
>
> >  library("AgiMicroRna")
> >  targets.micro=readTargets(infile="targets.txt", verbose=TRUE)
>
>Target File
>                FileName Treatment GErep Subject
>36_DMSO_1 36_DMSO_1.txt    36DMSO     1       1
>36_DMSO_2 36_DMSO_2.txt    36DMSO     1       2
>36_DMSO_3 36_DMSO_3.txt    36DMSO     1       3
>36_TCDD_1 36_TCDD_1.txt    36TCDD     2       1
>36_TCDD_2 36_TCDD_2.txt    36TCDD     2       2
>36_TCDD_3 36_TCDD_3.txt    36TCDD     2       3
>60_DMSO_1 60_DMSO_1.txt    60DMSO     3       1
>60_DMSO_2 60_DMSO_2.txt    60DMSO     3       2
>60_DMSO_3 60_DMSO_3.txt    60DMSO     3       3
>60_TCDD_1 60_TCDD_1.txt    60TCDD     4       1
>60_TCDD_2 60_TCDD_2.txt    60TCDD     4       2
>60_TCDD_3 60_TCDD_3.txt    60TCDD     4       3
>
> > ddaux=read.maimages(files=targets.micro$FileName,source="agilent",
>+
>+ 
>other.columns=list(IsGeneDetected="gIsGeneDetected",
>+
>+ 
>IsSaturated="gIsSaturated",
>+
>+ 
>IsFeatNonUnifOF="gIsFeatNonUnifOL",
>+
>+ 
>IsFeatPopnOL="gIsFeatPopnOL",
>+
>+ 
>ChrCoord="chr_coord",
>+
>+ 
>BGKmd="gBGMedianSignal",
>+
>+ 
>BGKus="gBGUsed"),
>+
>+                         columns=list(Rf="gTotalGeneSignal",
>+
>+ 
>Gf="gTotalProbeSignal",
>+
>+                                                        Rb="gMeanSignal",
>+
>+ 
>Gb="gProcessedSignal"),
>+
>+                         verbose=TRUE,sep="\t",quote="")
>Read 36_DMSO_1.txt
>Read 36_DMSO_2.txt
>Read 36_DMSO_3.txt
>Read 36_TCDD_1.txt
>Read 36_TCDD_2.txt
>Read 36_TCDD_3.txt
>Read 60_DMSO_1.txt
>Read 60_DMSO_2.txt
>Read 60_DMSO_3.txt
>Read 60_TCDD_1.txt
>Read 60_TCDD_2.txt
>Read 60_TCDD_3.txt
> > names(ddaux)
>[1] 
>"R"       "G"       "Rb"      "Gb"      "targets" "genes"   "source"  "other"
> > names(ddaux$genes)
>  [1] 
> "Row"            "Col"            "Start" 
>     "Sequence"       "ProbeUID"       "ControlType"
>  [7] "ProbeName"      "GeneName"       "SystematicName" "Description"
>
> > dd=readMicroRnaAFE(targets.micro, verbose=TRUE)
>Read 36_DMSO_1.txt
>Read 36_DMSO_2.txt
>Read 36_DMSO_3.txt
>Read 36_TCDD_1.txt
>Read 36_TCDD_2.txt
>Read 36_TCDD_3.txt
>Read 60_DMSO_1.txt
>Read 60_DMSO_2.txt
>Read 60_DMSO_3.txt
>Read 60_TCDD_1.txt
>Read 60_TCDD_2.txt
>Read 60_TCDD_3.txt
>
>   RGList:
>         dd$R:           'gTotalGeneSignal'
>         dd$G:           'gTotalProbeSignal'
>         dd$Rb:          'gMeanSignal'
>         dd$Gb:          'gProcessedSignal'
>
> > dd$genes=ddaux$genes[,c(6,7,8)]
> > cvArray(dd, "MeanSignal", targets.micro, verbose=TRUE)
>Foreground: MeanSignal
>
>         FILTERING BY ControlType FLAG
>
>  RAW DATA:                      5335
>  PROBES without CONTROLS:       4620
>----------------------------------
>   (Non-CTRL) Unique Probe:  490
>   (Non-CTRL) Unique Genes:  231
>----------------------------------
>DISTRIBUTION OF REPLICATED NonControl Probes
>reps
>   5   6   7  10
>  20  18  36 416
>------------------------------------------------------
>Replication at Probe level- MEDIAN  CV
>36_DMSO_1 36_DMSO_2 36_DMSO_3 36_TCDD_1 
>36_TCDD_2 36_TCDD_3 60_DMSO_1 60_DMSO_2 60_DMSO_3 60_TCDD_1 60_TCDD_2
>     0.078     0.081     0.091     0.081 
> 0.077     0.067     0.076     0.066     0.103     0.073     0.086
>60_TCDD_3
>     0.069
>------------------------------------------------------
>DISTRIBUTION OF REPLICATED Noncontrol Genes
>reps
>  20
>231
>------------------------------------------------------
> > ddTGS.rma = rmaMicroRna(dd, normalize=TRUE, background=FALSE)
>Calculating Expression
> > ddPROC = filterMicroRna(ddTGS.rma, dd, 
> control = TRUE, IsGeneDetected = TRUE, 
> wellaboveNEG = FALSE, limIsGeneDetected = 50, 
> limNEG = 25, makePLOT = FALSE, targets.micro, verbose = TRUE)
>FILTERING PROBES BY FLAGS
>
>
>FILTERING BY ControlType
>Error in data.frame(as.character(PROBE_ID), 
>as.character(GENE_ID), as.character(probe.chr),  :
>   arguments imply differing number of rows: 231, 0
>
>
>
>
>On Jun 2, 2010, at 5:32 AM, Pedro López Romero wrote:
>
> > Hi Neel,
> > Try to use 
> readMicroRnaAFE(targets,verbose=TRUE) to load 
> your data into R instead of calling 
> read.maimages() by yourself. This will solve your problem
> >
> > Cheers
> >
> > p.-
> >
> >
> > -----Mensaje original-----
> > De: Neel Aluru [mailto:naluru@whoi.edu]
> > Enviado el: Tuesday, June 01, 2010 7:34 PM
> > Para: Martin Morgan
> > CC: bioc; Pedro López Romero
> > Asunto: Re: [BioC] AgiMicroRna - FilterMicroRna question
> >
> > Thanks, Martin. I have contacted Pedro today 
> and hopefully he will get a chance to see my 
> mail. In the mean time I will follow your suggestions.
> >
> > Thanks once again.
> >
> > Neel
> >
> > On Jun 1, 2010, at 1:31 PM, Martin Morgan wrote:
> >
> >> On 06/01/2010 06:43 AM, Neel Aluru wrote:
> >>> Hello,
> >>>
> >>> I have asked this question before and 
> haven't heard from anyone. Sorry for reposting 
> it as I spent lot of time on it and still 
> cannot figure it out. I need to filter the data 
> before statistical analysis so as to remove the genes that are not detected.
> >
> >>>
> >>>> ddPROC = filterMicroRna(ddTGS.rma, dd.micro, control = TRUE,
> >>> IsGeneDetected = TRUE, wellaboveNEG = FALSE, limIsGeneDetected = 50,
> >>> limNEG = 25, makePLOT = FALSE, targets.micro, verbose = TRUE)
> >>> FILTERING PROBES BY FLAGS
> >>>
> >>>
> >>> FILTERING BY ControlType
> >>> Error in matrix(ddFILT$other$gIsGeneDetected, nrow = dim(ddFILT)[1],
> >>> ncol = dim(ddFILT)[2]) :
> >>> attempt to set an attribute on NULL
> >>>
> >>>
> >>> I checked my data files to see if the 
> required column (IsGeneDetected) is present and 
> it is there. But, for some reason it is not 
> detecting and I do not understand the error 
> message I am getting. If anyone can explain the 
> error message to me that would be great. I have posted the session info below.
> >>
> >> Hi Neel -- I can't help with specifics, but
> >>
> >>> matrix(NULL)
> >> Error in matrix(NULL) : attempt to set an attribute on NULL
> >>
> >> so the proximate cause of the error message is likely that
> >> ddFILT$other$gIsGeneDetected is equal to NULL, e.g., because it doesn't
> >> exist. You can investigate this by inspecting the code, e.g.,
> >>
> >>> options(error=browser())
> >>
> >> and then re-running your code. See ?browser; when done use
> >> options(error=NULL). Before that I'd revisit the help page for this
> >> function and double-check that you are providing appropriate arguments.
> >>
> >> I've added
> >>
> >>> packageDescription('AgiMicroRna')$Maintainer
> >> [1] "Pedro Lopez-Romero <plopez@cnic.es>"
> >>
> >> to the email, as Pedro in the best position to help you.
> >>
> >> Martin
> >>
> >>> Thank you very much,
> >>>
> >>> Neel
> >>>
> >>>
> >>>
> >>>
> >>> Session Info
> >>>
> >>>> library("AgiMicroRna")
> >>>> targets.micro=readTargets(infile="targets.txt", verbose=TRUE)
> >>>
> >>> Target File
> >>>              FileName Treatment GErep Subject
> >>> 36_DMSO_1 36_DMSO_1.txt    36DMSO     1       1
> >>> 36_DMSO_2 36_DMSO_2.txt    36DMSO     1       2
> >>> 36_DMSO_3 36_DMSO_3.txt    36DMSO     1       3
> >>> 36_TCDD_1 36_TCDD_1.txt    36TCDD     2       1
> >>> 36_TCDD_2 36_TCDD_2.txt    36TCDD     2       2
> >>> 36_TCDD_3 36_TCDD_3.txt    36TCDD     2       3
> >>> 60_DMSO_1 60_DMSO_1.txt    60DMSO     3       1
> >>> 60_DMSO_2 60_DMSO_2.txt    60DMSO     3       2
> >>> 60_DMSO_3 60_DMSO_3.txt    60DMSO     3       3
> >>> 60_TCDD_1 60_TCDD_1.txt    60TCDD     4       1
> >>> 60_TCDD_2 60_TCDD_2.txt    60TCDD     4       2
> >>> 60_TCDD_3 60_TCDD_3.txt    60TCDD     4       3
> >>>
> >>>> dd.micro=read.maimages(targets.micro$FileName,
> >>> columns=list(R="gTotalGeneSignal",G=
> >>> "gTotalProbeSignal",Rb="gMeanSignal", Gb="gProcessedSignal"),
> >>> 
> annotation=c("ProbeUID","ControlType","ProbeName","GeneName","SystematicName",
> >>> "sequence", "accessions","probe_mappings",
> >>> "gIsGeneDetected","gIsSaturated","gIsFeatNonUnifOL",
> >>> "gIsFeatPopnOL","chr_coord","gBGMedianSignal","gBGUsed"))
> >>> Read 36_DMSO_1.txt
> >>> Read 36_DMSO_2.txt
> >>> Read 36_DMSO_3.txt
> >>> Read 36_TCDD_1.txt
> >>> Read 36_TCDD_2.txt
> >>> Read 36_TCDD_3.txt
> >>> Read 60_DMSO_1.txt
> >>> Read 60_DMSO_2.txt
> >>> Read 60_DMSO_3.txt
> >>> Read 60_TCDD_1.txt
> >>> Read 60_TCDD_2.txt
> >>> Read 60_TCDD_3.txt
> >>>> cvArray(dd.micro, "MeanSignal", targets.micro, verbose=TRUE)
> >>> Foreground: MeanSignal
> >>>
> >>>       FILTERING BY ControlType FLAG
> >>>
> >>> RAW DATA:                       5335
> >>> PROBES without CONTROLS:        4620
> >>> ----------------------------------
> >>> (Non-CTRL) Unique Probe:  490
> >>> (Non-CTRL) Unique Genes:  231
> >>> ----------------------------------
> >>> DISTRIBUTION OF REPLICATED NonControl Probes
> >>> reps
> >>> 5   6   7  10
> >>> 20  18  36 416
> >>> ------------------------------------------------------
> >>> Replication at Probe level- MEDIAN  CV
> >>> 36_DMSO_1 36_DMSO_2 36_DMSO_3 36_TCDD_1 36_TCDD_2 36_TCDD_3 60_DMSO_1
> >>> 60_DMSO_2 60_DMSO_3
> >>>   0.078     0.081     0.091     0.081     0.077     0.067
> >>> 0.076     0.066     0.103
> >>> 60_TCDD_1 60_TCDD_2 60_TCDD_3
> >>>   0.073     0.086     0.069
> >>> ------------------------------------------------------
> >>> DISTRIBUTION OF REPLICATED Noncontrol Genes
> >>> reps
> >>> 20
> >>> 231
> >>> ------------------------------------------------------
> >>>> ddTGS.rma = rmaMicroRna(dd.micro, normalize=TRUE, background=FALSE)
> >>> Calculating Expression
> >>>> ddPROC = filterMicroRna(ddTGS.rma, dd.micro, control = TRUE,
> >>> IsGeneDetected = TRUE, wellaboveNEG = FALSE, limIsGeneDetected = 50,
> >>> limNEG = 25, makePLOT = FALSE, targets.micro, verbose = TRUE)
> >>> FILTERING PROBES BY FLAGS
> >>>
> >>>
> >>> FILTERING BY ControlType
> >>> Error in matrix(ddFILT$other$gIsGeneDetected, nrow = dim(ddFILT)[1],
> >>> ncol = dim(ddFILT)[2]) :
> >>> attempt to set an attribute on NULL
> >>>
> >>>> MMM = ddTGS.rma$Rb
> >>>> colnames(MMM) = colnames(dd.micro$Rb)
> >>>> maintitle='TGS.rma'
> >>>> colorfill='blue'
> >>>> ddaux=ddTGS.rma
> >>>> ddaux$G=MMM
> >>>> mvaMicroRna(ddaux, maintitle, verbose=TRUE)
> >>>
> >>> ------------------------------------------------------
> >>> mvaMicroRna info:
> >>> FEATURES :      231
> >>> POSITIVE CTRL:          12
> >>> NEGATIVE CTRL:          7
> >>> STRUCTURAL:             3
> >>>> rm(ddaux)
> >>>> RleMicroRna(MMM,"RLE TGS.rma", colorfill)
> >>>> boxplotMicroRna(MMM, maintitle, colorfill)
> >>>> plotDensityMicroRna(MMM, maintitle)
> >>>> spottypes = readSpotTypes()
> >>>> ddTGS.rma$genes$Status = controlStatus(spottypes, ddTGS.rma)
> >>> Matching patterns for: ProbeName GeneName
> >>> Found 231 gene
> >>> Found 1 BLANK
> >>> Found 1 Blank
> >>> Found 0 blank
> >>> Found 6 positive
> >>> Found 0 negative
> >>> Found 0 flag1
> >>> Found 0 flag2
> >>> Found 6 flag3
> >>> Found 5 flag4
> >>> Found 1 flag5
> >>> Setting attributes: values
> >>>> i = ddTGS.rma$genes$Status == "gene"
> >>>> esetPROC = esetMicroRna(ddTGS.rma[i,], targets.micro,
> >>> makePLOT=TRUE, verbose = TRUE)
> >>> outPUT DATA: esetPROC
> >>> Features  Samples
> >>>    231       12
> >>>> design=model.matrix(~-1+treatment)
> >>>> print(design)
> >>>  treatment36DMSO treatment36TCDD treatment60DMSO treatment60TCDD
> >>> 1                1               0               0               0
> >>> 2                1               0               0               0
> >>> 3                1               0               0               0
> >>> 4                0               1               0               0
> >>> 5                0               1               0               0
> >>> 6                0               1               0               0
> >>> 7                0               0               1               0
> >>> 8                0               0               1               0
> >>> 9                0               0               1               0
> >>> 10               0               0               0               1
> >>> 11               0               0               0               1
> >>> 12               0               0               0               1
> >>> attr(,"assign")
> >>> [1] 1 1 1 1
> >>> attr(,"contrasts")
> >>> attr(,"contrasts")$treatment
> >>> [1] "contr.treatment"
> >>>
> >>>> fit=lmFit(esetPROC, design)
> >>>> cont.matrix = makeContrasts(treatment36TCDDvstreatment36DMSO =
> >>> treatment36TCDD-treatment36DMSO, treatment60TCDDvstreatment60DMSO =
> >>> treatment60TCDD-treatment60DMSO,treatment60TCDDvstreatment36TCDD =
> >>> treatment60TCDD-treatment36TCDD, treatment60DMSOvstreatment36DMSO =
> >>> treatment60DMSO-treatment36DMSO, levels=design)
> >>>> print(cont.matrix)
> >>>                Contrasts
> >>> Levels            treatment36TCDDvstreatment36DMSO
> >>> treatment60TCDDvstreatment60DMSO
> >>> treatment36DMSO                               -1
> >>>            0
> >>> treatment36TCDD                                1
> >>>            0
> >>> treatment60DMSO                                0
> >>>           -1
> >>> treatment60TCDD                                0
> >>>            1
> >>>                Contrasts
> >>> Levels            treatment60TCDDvstreatment36TCDD
> >>> treatment60DMSOvstreatment36DMSO
> >>> treatment36DMSO                                0
> >>>           -1
> >>> treatment36TCDD                               -1
> >>>            0
> >>> treatment60DMSO                                0
> >>>            1
> >>> treatment60TCDD                                1
> >>>            0
> >>>> fit2 = contrasts.fit(fit,cont.matrix)
> >>>> print(head(fit2$coeff))
> >>>           Contrasts
> >>>            treatment36TCDDvstreatment36DMSO 
> treatment60TCDDvstreatment60DMSO
> >>> 
> dre-let-7a                      0.038640984                      0.013333873
> >>> 
> dre-let-7b                      0.074038749                     -0.031608286
> >>> 
> dre-let-7c                      0.026244357                     -0.005682488
> >>> 
> dre-let-7d                      0.067340768                      0.055567054
> >>> 
> dre-let-7e                      0.004569306                      0.136348664
> >>> 
> dre-let-7f                      0.042880109                      0.085568058
> >>>           Contrasts
> >>>            treatment60TCDDvstreatment36TCDD 
> treatment60DMSOvstreatment36DMSO
> >>> 
> dre-let-7a                        1.7358343                       1.76114142
> >>> 
> dre-let-7b                        0.1366920                       0.24233899
> >>> 
> dre-let-7c                        0.9920976                       1.02402449
> >>> 
> dre-let-7d                        0.8098432                       0.82161694
> >>> 
> dre-let-7e                        0.1186829                      -0.01309647
> >>> 
> dre-let-7f                        1.1245878                       1.08189990
> >>>> fit2 = eBayes(fit2)
> >>>> fit2 = basicLimma(esetPROC, design, cont.matrix, verbose = TRUE)
> >>> DATA
> >>> Features  Samples
> >>>    231       12
> >>>
> >>>> DE = getDecideTests(fit2, DEmethod = "separate", MTestmethod =
> >>> "BH", PVcut = 0.1, verbose = TRUE)
> >>>
> >>> ------------------------------------------------------
> >>> Method for Selecting DEGs: separate
> >>> Multiple Testing  method:  BH - pval 0.1
> >>>
> >>>    treatment36TCDDvstreatment36DMSO treatment60TCDDvstreatment60DMSO
> >>> UP                                  0                                5
> >>> DOWN                                0                                1
> >>>    treatment60TCDDvstreatment36TCDD treatment60DMSOvstreatment36DMSO
> >>> UP                                 56                               51
> >>> DOWN                               80                               91
> >>> ------------------------------------------------------
> >>>> pvalHistogram(fit2, DE, PVcut = 0.1, DEmethod ="separate",
> >>> MTestmethod="BH",cont.matrix, verbose= TRUE)
> >>>> significantMicroRna(esetPROC, ddTGS.rma, targets.micro, fit2,
> >>> cont.matrix, DE, DEmethod = "separate", MTestmethod= "BH", PVcut =
> >>> 0.1, Mcut=0, verbose=TRUE)
> >>> ------------------------------------------------------
> >>> CONTRAST:  1  -  treatment36TCDDvstreatment36DMSO
> >>>
> >>> Error in data.frame(PROBE_ID, as.character(GENE_ID),
> >>> as.character(chr_coord),  :
> >>> arguments imply differing number of rows: 231, 0
> >>>
> >>>
> >>>
> >>>
> >>> Neel Aluru
> >>> Postdoctoral Scholar
> >>> Biology Department
> >>> Woods Hole Oceanographic Institution
> >>> Woods Hole, MA 02543
> >>> USA
> >>> 508-289-3607
> >>>
> >>> _______________________________________________
> >>> Bioconductor mailing list
> >>> Bioconductor@stat.math.ethz.ch
> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>> Search the archives: 
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >>
> >> --
> >> Martin Morgan
> >> Computational Biology / Fred Hutchinson Cancer Research Center
> >> 1100 Fairview Ave. N.
> >> PO Box 19024 Seattle, WA 98109
> >>
> >> Location: Arnold Building M1 B861
> >> Phone: (206) 667-2793
> >>
> >
> > Neel Aluru
> > Postdoctoral Scholar
> > Biology Department
> > Woods Hole Oceanographic Institution
> > Woods Hole, MA 02543
> > USA
> > 508-289-3607
> >
> >
> >
> >
> > *************** AVISO LEGAL ***************
> > Este mensaje va dirigido, de manera exclusiva, a su destinatario y
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> > Asimismo, le comunicamos que la distribución, copia o utilización de
> > este mensaje, o de cualquier documento adjunto al mismo, cualquiera
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> > como destinatario de este mensaje, que el correo electrónico y las
> > comunicaciones por medio de Internet no permiten asegurar ni
> > garantizar la confidencialidad de los mensajes transmitidos, así como
> > tampoco su integridad o su correcta recepción, por lo que el CNIC no
> > asume responsabilidad alguna por tales circunstancias. Si no
> > consintiese la utilización del correo electrónico o de las
> > comunicaciones vía Internet le rogamos nos lo comunique y ponga en
> > nuestro conocimiento de manera inmediata.
> >
> > *************** LEGAL NOTICE **************
> > This message is intended exclusively for the person to whom it is
> > addressed and contains privileged and confidential information
> > protected from disclosure by law. If you are not the addressee
> > indicated in this message, you should immediately delete it and any
> > attachments and notify the sender by reply e-mail or by phone
> > (+34 914531200). In such case, you are hereby notified that any
> > dissemination, distribution, copying or use of this message or any
> > attachments, for any purpose, is strictly prohibited by law. We
> > hereby inform you, as addressee of this message, that e-mail and
> > Internet do not guarantee the confidentiality, nor the completeness
> > or proper reception of the messages sent and, thus, CNIC does not
> > assume any liability for those circumstances. Should you not agree
> > to the use of e-mail or to communications via Internet, you are
> > kindly requested to notify us immediately.
> >
>
>Neel Aluru
>Postdoctoral Scholar
>Biology Department
>Woods Hole Oceanographic Institution
>Woods Hole, MA 02543
>USA
>508-289-3607
>
>
>
>
>*************** AVISO LEGAL ***************
>Este mensaje va dirigido, de manera exclusiva, a su destinatario y
>contiene información confidencial y sujeta al secreto profesional,
>cuya divulgación no está permitida por la ley. En caso de haber
>recibido este mensaje por error, le rogamos que, de forma inmediata,
>nos lo comunique mediante correo electrónico remitido a nuestra
>atención o a través del teléfono (+34 914531200) y proceda a su
>eliminación, así como a la de cualquier documento adjunto al mismo.
>Asimismo, le comunicamos que la distribución, copia o utilización de
>este mensaje, o de cualquier documento adjunto al mismo, cualquiera
>que fuera su finalidad, están prohibidas por la ley. Le informamos,
>como destinatario de este mensaje, que el correo electrónico y las
>comunicaciones por medio de Internet no permiten asegurar ni
>garantizar la confidencialidad de los mensajes transmitidos, así como
>tampoco su integridad o su correcta recepción, por lo que el CNIC no
>asume responsabilidad alguna por tales circunstancias. Si no
>consintiese la utilización del correo electrónico o de las
>comunicaciones vía Internet le rogamos nos lo comunique y ponga en
>nuestro conocimiento de manera inmediata.
>
>*************** LEGAL NOTICE **************
>This message is intended exclusively for the person to whom it is
>addressed and contains privileged and confidential information
>protected from disclosure by law. If you are not the addressee
>indicated in this message, you should immediately delete it and any
>attachments and notify the sender by reply e-mail or by phone
>(+34 914531200). In such case, you are hereby notified that any
>dissemination, distribution, copying or use of this message or any
>attachments, for any purpose, is strictly prohibited by law. We
>hereby inform you, as addressee of this message, that e-mail and
>Internet do not guarantee the confidentiality, nor the completeness
>or proper reception of the messages sent and, thus, CNIC does not
>assume any liability for those circumstances. Should you not agree
>to the use of e-mail or to communications via Internet, you are
>kindly requested to notify us immediately.

Neel Aluru Ph.D.
Post doctoral Scholar
Biology Department
Redfield 304 (MS#32)
Woods Hole Oceanographic Institution
Woods Hole MA 02543 USA
Phone: (508) 289-3607 [Office]
774-392-3727 [Cell]
RID: A-7237-2009  
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