[BioC] Moderated t-test

[Wang, Li]

Dear list members

I am confronted with an error when doing hierarchical clustering for expression value clustering in R. 

> d <- dist(n, method="euclidean")
Warning message:
In dist(n, method = "euclidean") : NAs introduced by coercion
> h <- hclust(d, method="ward")
Error in hclust(d, method = "ward") : 
  NA/NaN/Inf in foreign function call (arg 11)

It seems that the NAs in my raw data affect it.  
I tried to remove NAs with the following two ways:
d <- na.omit(d)
d <- d[rowSums(!is.na(d))!=0, colSums(!is.na(d))!=0]

However, they didnot solve the problem.

Any comments and suggestions are very appreciated.

Thanks!
Li
________________________________________
From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] On Behalf Of Ekta Jain [Ekta_Jain at jubilantbiosys.com]
Sent: Tuesday, May 15, 2012 12:13 AM
To: Chintanu
Cc: bioconductor at r-project.org
Subject: Re: [BioC] Moderated t-test

Hi Chintanu,
Sorry I went underground for a short time., not sure if you have solved your problem but sharing some info here incase it helps.

If you sort your toptable in R it will sort everything except the row names. If you fit the annotation on your data before you  do toptable it will sort all your data.

If you find it easier you can sort toptable after you write it out to an .xls file and use cbind() without the sort in R.

Best,
Ekta

From: Chintanu [mailto:chintanu at gmail.com]
Sent: 10 May 2012 10:04
To: bioconductor at r-project.org
Cc: Ekta Jain
Subject: Re: Moderated t-test

Hi,

Not sure whether that answers my question.
In case I haven't been able to put forward the question correctly, I am trying it here again:

fit <- lmFit(file[,-1], design=group) # Column 1 contains row-names, which are the gene/feature names.

# Above, each of the output of the object, fit would refer to the corresponding gene/feature name.

fit2 <- eBayes(fit)
tt <- topTable(fit2, number=Inf, adjust.method="BH")$t

# Now, when topTable() is applied, the question is -

# will it sort the data along with column 1 (that contains row/gene/feature names) such that it is then just a matter of retrieving the data corresponding to the respective genes using function like cbind ().

# OR

# Will topTable() sort everything EXCEPT column 1 ? If this happens, applying functions like cbind() will pick wrong combinations.

Cheers,

Chintanu


=========================================================================
On Wed, May 9, 2012 at 4:31 PM, Ekta Jain <Ekta_Jain at jubilantbiosys.com<mailto:Ekta_Jain at jubilantbiosys.com>> wrote:
Hi,
The cbind function combines data frames column wise - you should read here http://www.stat.ucl.ac.be/ISdidactique/Rhelp/library/base/html/cbind.html
Or
>?cbind on your R console.

Toptable will only give you the a subset of the entire data i.e the top genes in which genes are ranked according to the F-statistic for that set of contrasts. To get 'toptable' results for all your genes you could do something like:
>numGenes <- rownames(file[,1])
> toptableOut<- topTable(fit2, number=Inf, adjust.method="BH", number = numGenes)$t

Best,
-Ekta


From: Chintanu [mailto:chintanu at gmail.com<mailto:chintanu at gmail.com>]
Sent: 09 May 2012 11:49
To: Ekta Jain
Cc: bioconductor at r-project.org<mailto:bioconductor at r-project.org>
Subject: Re: Moderated t-test

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 at jubilantbiosys.com<mailto:Ekta_Jain at 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 at r-project.org<mailto:bioconductor-bounces at r-project.org> [mailto:bioconductor-bounces at r-project.org<mailto:bioconductor-bounces at 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
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