## User: Seymoo

Seymoo0
Reputation:
0
Status:
New User
Last seen:
3 months, 1 week ago
Joined:
2 years, 7 months ago
Email:
h**********@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

#### Posts by Seymoo

<prev • 31 results • page 1 of 4 • next >
1
138
views
1
Comment: C: Install a custom CDF file
... Great! I downloaded the annotation and converted it to a data frame z <-z @dataTable@table. I did follow your steps and excluded rows in **z** without available **EntrezGeneID**. But now **dim(z)=41090** and table(isUnique(z$EntrezGeneID))shows **29109** non unique values. this is not usual ... written 3 months ago by Seymoo0 1 answer 138 views 1 answers Comment: C: Install a custom CDF file ... Thanks a lot James! I did try your solution but I just replaced **ReadAffy** with **affy::justRMA** and used **cdfname = "hursta2a520709cdf, normalize = TRUE"** and now it seems that I have a log2 transformed expression matrix.However, I am not sure if the rows (**n=60607**) are converted to ... written 3 months ago by Seymoo0 1 answer 138 views 1 answer ... I would like to access gene level expression data from **GSE131418** study. However, since it is not possbile to do that with "GEOquery" for some reason, I want to use the CDF file "**GPL15048_HuRSTA_2a520709.CDF.gz**" provided under "**GSE131418_RAW.tar**" to perform RMA normalization and probe s ... written 3 months ago by Seymoo0 • updated 3 months ago by James W. MacDonald51k 0 answers 222 views 0 answers ... I have noticed that when I apply NMF to log2 transformed gene expression data for classification purpose the result are different than if I first do an exponential transformation of the same data matrix. Also, test statistics increase after exponential transformation. I know that NMF is not applica ... written 16 months ago by Seymoo0 0 answers 263 views 0 answers ... I am wondering how to make a silhouette plot on the results from Mclust packge, where measure of silhouette for each sample in each group is shown? Using "Fcp" package I can check the average silhouette. mb = Mclust(iris[,-5], 3) cs = cluster.stats(dist(iris[1:4]), mb$classification) #instal ...
written 19 months ago by Seymoo0
2
2.1k
views
2
Comment: C: limma contrast matrix
... Hi @Aaron Lun . I didnt want to post a new question because I am actually a bit confused with the reversing that you just mentioned above ( e.g., N50_C - N50_D instead of N50_D - N50_C ), because by doing so this can swap the number of detected DE. I am wondering if what is generally accepted when I ...
written 19 months ago by Seymoo0
1
400
views
1
... Thanks James! ...
written 20 months ago by Seymoo0
1
400
views
1
... I want to use camera function in limma. I downloaded xml file from MSigDB and loaded it but I am wondering how can I make it to a compatible list for camera function as it has been mentioned in here that GEneCollection need to be converted to a list. what I have done is gsc <- getBroadSets(" ...
written 20 months ago by Seymoo0 • updated 20 months ago by James W. MacDonald51k
0
245
views
0
... I have a gene expression data AllExp and a data.frame info with sample name of AllExp as row names and first column in it specifies groups that each sample belongs to. I am trying to perform a a gene set enrichment analysis using GSA package. but I get following error `Error in cut.default(s ...
written 20 months ago by Seymoo0
2
491
views
2
... @saibar Hi Sara, Thanks for making this great package. I am wondering if you add cost argument in the formula to be set by users or if you could explain how to modify it the way it is right now ? I am using Caret package to find optimal cost to be used in the function and I would like to adjust co ...
written 22 months ago by Seymoo0

#### Latest awards to Seymoo

No awards yet. Soon to come :-)

Content
Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.