Hi Ekta,

Thank you.

However, my worry is that -

whether topTable() will shuffle & sort the dataframe (except the row names
of 1st column) such that when cbind() is eventually applied, it will only
join the individual test outputs with the incorrect row-names !!

Cheers,
Chintanu


=================================================================


On Wed, May 9, 2012 at 4:06 PM, Ekta Jain <Ekta_Jain@jubilantbiosys.com>wrote:

> Hi Chintanu,
> You can use the cbind function.
>
> > toptableOut<- topTable(fit2, number=Inf, adjust.method="BH")$t
> > x <- cbind(file[,1],toptableOut)
> ## the (file[,1] will get you all rows for column 1
> > write.table(x,"<filename>.txt", quote=F, row.names=FALSE, sep="\t")
>
> Hope this helps,
> Ekta
>
> -----Original Message-----
> From: bioconductor-bounces@r-project.org [mailto:
> bioconductor-bounces@r-project.org] On Behalf Of Chintanu
> Sent: 09 May 2012 11:21
> To: bioc
> Subject: [BioC] Moderated t-test
>
> Hi,
>
> I am trying to do a moderated t-test on two groups of samples as follows -
>
> file <- read.csv (file.choose(), header = TRUE) # Column 1 contains
> row-names
>
> group <- rep(0:1, c(3,5))
>
> library (limma)
>
> fit <- lmFit(file[,-1], design=group)  # Column 1 contains row-names
>
> fit2 <- eBayes(fit)
>
> topTable(fit2, number=Inf, adjust.method="BH")$t
>
> I am not sure how to obtain the values of topTable() along with the
> corresponding row names.
>
> Could you please advise.
>
> Thank you.
>
> Cheers,
> Chintanu
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> The information contained in this electronic message and in any
> attachments to this message is confidential, legally privileged and
> intended only for use by the person or entity to which this electronic
> message is addressed. If you are not the intended recipient, and have
> received this message in error, please notify the sender and system manager
> by return email and delete the message and its attachments and also you are
> hereby notified that any distribution, copying, review, retransmission,
> dissemination or other use of this electronic transmission or the
> information contained in it is strictly prohibited. Please note that any
> views or opinions presented in this email are solely those of the author
> and may not represent those of the Company or bind the Company. Any
> commitments made over e-mail are not financially binding on the company
> unless accompanied or followed by a valid purchase order. This message has
> been scanned for viruses and dangerous content by Mail Scanner, and is
> believed to be clean. The Company accepts no liability for any damage
> caused by any virus transmitted by this email.
> www.jubl.com
>
>

	[[alternative HTML version deleted]]

