Question: microarray data analysis
0
gravatar for au.rinki.bio
16 months ago by
au.rinki.bio10
au.rinki.bio10 wrote:

I am working on microarray data analysis. to find out DE gene i have use p value <0.05. now i want to go with Benjamini-Hochberg correction, for this i have use samr package in R. for filtering significant genes delta value must be given by users. plz suggest me range of delta value and also give information about what is q value? how it is useful for Differential expression analysis of gene?

ADD COMMENTlink modified 16 months ago by arta540 • written 16 months ago by au.rinki.bio10
2

If you're working in R, are you using limma? and if so, why didn't you filter based on adjusted-p-value (the BH correction will have been done for you) instead of p-value.

ADD REPLYlink written 16 months ago by russhh4.3k
1

Hi au.rinki.bio,

Please chose a more descriptive title of your threads, "microarray data analysis" doesn't say a lot. "Multiple testing correction" is something you should have included, for example.

In addition, please give feedback on your previous question(s):
If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

Cheers,
Wouter

ADD REPLYlink written 16 months ago by WouterDeCoster38k

thank you. i would follow your sugestion.

ADD REPLYlink written 16 months ago by au.rinki.bio10
3
gravatar for arta
16 months ago by
arta540
Sweden
arta540 wrote:

The reason why you are correcting the p values is multiple testing. In microarray data there are around 20.000 genes, as rows. So you do 20.000 times testing whether the gene is significantly DE. When you set your p value to 0.05, 1000 genes (20000 * 0.05) are significantly differentially expressed by chance. To avoid getting false positives or type-1 error, you correct your p values. Corrected p-values are generally called adjusted p values and q value is p value which is adjusted for False Discovery Rate (FDR).

To do that in R, you do not need to use any extra package. Following function will do the same job.

p.adjust(p.values, method = "BH", n = length(p.values))
ADD COMMENTlink written 16 months ago by arta540

i am using following command line and use affy package.

library(makecdfenv)
library(affyio)
library(affy)
ovarian<-make.cdf.env("HGU133A_Hs_ENSG.cdf")
data<-ReadAffy(cdfname='ovarian')
data
eset<-rma(data)
exprSet <- exprs(eset)
pvalue.exprSet = apply(exprSet, 1, function(x){t.test(x[1:4], x[5:45]) $p.value}) 
Combine.exprset.pvalue = cbind(exprSet,pvalue.exprSet)
write.table(Combine.exprset.pvalue,"NormalizedValues.xls",sep="\t",col.names = NA)
ADD REPLYlink modified 16 months ago by WouterDeCoster38k • written 16 months ago by au.rinki.bio10
1

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

ADD REPLYlink written 16 months ago by WouterDeCoster38k

when i am using command suggested by you after p value calculation following error occur-

p.adjust(p.values, method = "BH", n = length(p.values))
Error in p.adjust(p.values, method = "BH", n = length(p.values)) : 
  object 'p.values' not found
Error during wrapup: cannot open the connection
ADD REPLYlink modified 16 months ago by WouterDeCoster38k • written 16 months ago by au.rinki.bio10

thank you so much. but here is one more question what should be the range of thresold for agjusted p -value?

ADD REPLYlink written 16 months ago by au.rinki.bio10
2

Based on your text above, the threshold should be 0.05. Can I strongly suggest that you read and work through the limma user's guide rather than doing the unmoderated t-tests that you've proposed. And by strongly suggest, I mean, really strongly suggest.

ADD REPLYlink modified 16 months ago • written 16 months ago by russhh4.3k

thank you so much for suggestion.

ADD REPLYlink written 16 months ago by au.rinki.bio10

when i am using limma package their are a lots of error coming and not running proprely. kindly suggest me any tutorial for analysis of microarray data( CEL file) using limma package.

ADD REPLYlink written 16 months ago by au.rinki.bio10
1

In what way did it fail, and what have you done to work out why it failed? Here's a brusque tutorial I wrote: here

ADD REPLYlink written 16 months ago by russhh4.3k

thank you so much. but here is one more question what should be the range of thresold for agjusted p -value?

ADD REPLYlink written 16 months ago by au.rinki.bio10
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