Question: How To Select Only Human Mirnas From Affy Chip While Data Analysis Using R
1
gravatar for Shafi
6.2 years ago by
Shafi20
Shafi20 wrote:

I am new to R and want to analyze miRNA data set of 3 groups. I am able to normalize, designing matrix and contrast matrix and differential expression. But what I am facing is affy chip has lot of other miRNA probes which I guess I am not able to filter them out. I just want to select human miRNAs from chip and do analysis and compare the three groups. Can any one help me in this

gene affymetrix human mirna • 2.8k views
ADD COMMENTlink modified 6.2 years ago by Shafi10 • written 6.2 years ago by Shafi20

Shari, it would help to mention which Affy chip you are using. If they are annotated using miRBase annotations, then the human miRNA names should all start with "hsa"

ADD REPLYlink written 6.2 years ago by Qdjm1.9k

its mirrna20 from affymetrix

ADD REPLYlink written 6.2 years ago by Shafi20

topTable(fit2, coef=1, adjust="fdr", sort.by="B", number=20) ID logFC AveExpr t P.Value adj.P.Val B 20398 zma-miR156e_st 0.3198252 0.4998068 4.487144 3.782516e-05 0.6469183 0.62186254 18047 pvu-miR482-star_st -0.2559547 0.5195567 -4.233259 8.925328e-05 0.6469183 0.09110598 2995 ame-miR-316_st -0.3233149 0.4537794 -4.029978 1.748058e-04 0.6469183 -0.32656880 12019 hsa-miR-3119_st -0.3040332 0.4469291 -4.016812 1.824927e-04 0.6469183 -0.35336278 2088 ENSG00000252228_x_st -0.3748713 0.6650043 -3.990783 1.986619e-04 0.6

ADD REPLYlink written 6.2 years ago by Shafi20

you can not only has but others are dominant

ADD REPLYlink written 6.2 years ago by Shafi20

you can see not only has but other species are dominant in topTAble

ADD REPLYlink written 6.2 years ago by Shafi20

you can see not only has but other species are dominant in topTAble

ADD REPLYlink written 6.2 years ago by Shafi20

ExpressionSet (storageMode: lockedEnvironment) assayData: 20706 features, 55 samples element names: exprs protocolData sampleNames: EC1_(miRNA).CEL EC21_(miRNA).CEL ... YC85_(miRNA).CEL (55 total) varLabels: ScanDate varMetadata: labelDescription phenoData sampleNames: EC1_(miRNA).CEL EC21_(miRNA).CEL ... YC85_(miRNA).CEL (55 total) varLabels: sample varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' Annotation: mirna20

ADD REPLYlink written 6.2 years ago by Shafi20

Shafi, looks like you have "hsa" miRNAs. So filter out all miRNAs whose names don't start with hsa. Then count the number of miRNAs left -- if it's less than 300, you probably overfiltered and if its more than about 1500, you haven't filtered enough.

ADD REPLYlink written 6.2 years ago by Qdjm1.9k

yes that is what I want to do. Can you help me how I can select only has miRNAs? I appreciate you kind help

ADD REPLYlink written 6.2 years ago by Shafi20

yes that is what I want to do. Can you help me how I can select only has miRNAs? I appreciate you kind help

ADD REPLYlink written 6.2 years ago by Shafi20

yes that is what I want to do. Can you help me how I can select only "hsa" miRNAs? I appreciate you kind help

ADD REPLYlink written 6.2 years ago by Shafi20
2
gravatar for Agatha
6.2 years ago by
Agatha340
Agatha340 wrote:

If I understood correctly, you want to filter them out-> just the human miRNAs. You can use grep for that Here is an example (loads a fasta file containing the hairpins annotated in miRBase and filters the human ones)

library("Biostrings")
aux <- read.RNAStringSet("hairpin.fa")
names(aux)
grep("hsa",names(aux))
aux[grep("hsa",names(aux))]

You can adapt it for your task. Hope this helps.

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Agatha340
1

@Shafi- you cannot open the file since it is not saved locally on your computer. I do not have access to your code so I gave you an example on how to extract rows from a data object containing a specific substring, in this case, "hsa" the default start string for the miRNAs annotated in mirBase

ADD REPLYlink written 6.2 years ago by Agatha340

Error in .Call2("new_input_ExternalFilePtr", fp, PACKAGE = "Biostrings") : cannot open file 'hairpin.fa'

ADD REPLYlink written 6.2 years ago by Shafi20

Did not work! What should I do....

ADD REPLYlink written 6.2 years ago by Shafi20
0
gravatar for Shafi
6.2 years ago by
Shafi10
Shafi10 wrote:

Hi

I just want to study differential expression of human miRNAs and compare 3 gruops. I have used affy chips (mirna20). Just 2 weeks before I started learning R. Dont know much. During these days I learned how to load, read, normalize(RMA) data. I will appreciate if some one will help me out or direct me towards relevant example. Thanks in advance

ADD COMMENTlink written 6.2 years ago by Shafi10
0
gravatar for User 2925
6.1 years ago by
User 292510
User 292510 wrote:

Hello Agatha

would the same example code work with biopython? i have also a hairpin.fa file from miRbase and am only interested in the hsa-mir-*** miRNAs. how can i extract them with the id,and sequences?

ADD COMMENTlink written 6.1 years ago by User 292510
0
gravatar for Shafi
6.1 years ago by
Shafi10
Shafi10 wrote:

Hi

I am also new to R. I used following script to grep only human miRNAs.

# grep("hsa", featureNames(eset))->hsa

# eset.hsa<-eset[hsa,]

Hope it will work for you

ADD COMMENTlink written 6.1 years ago by Shafi10
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