User: anitabaery

gravatar for anitabaery
anitabaery0
Reputation:
0
Status:
New User
Last seen:
1 year, 4 months ago
Joined:
1 year, 6 months ago
Email:
a*********@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 anitabaery

<prev • 8 results • page 1 of 1 • next >
0
votes
1
answer
345
views
1
answer
Affy ClariomD human transcriptome annotation
... Hi All, I have annotated my data with anno<- annotateEset(rma, pd.clariom.d.human) however, I have noticed that there are ~6000 genes without chromosome and base positions assigned. I have checked and they do have position on NCBI (build37). Is it because the annotated file used for annotation ...
annotation affy pd.clariom.d.human written 17 months ago by anitabaery0 • updated 17 months ago by James W. MacDonald50k
0
votes
1
answer
606
views
1
answers
Comment: C: Clariom D Assays, annotation
... Hi again James, I have modified the lines and it worked: out$CHR = as.character(out$CHR) out$CHRLOC = as.character(out$CHRLOC) out = as.matrix(out) write.csv(out, "data.csv") However, I have 2 question 1. how to add CHRSTOP , I have tried CDSSTOP but had Error in .testForValidCols(x, cols) : ...
written 18 months ago by anitabaery0
0
votes
1
answer
606
views
1
answers
Comment: C: Clariom D Assays, annotation
... Hi James, I have tried df <- apply(df,5,as.character) fwrite(out, file ="..") out$col5 = as.character(out$col5) but nothing is working ... Can I also ask if the annotation is build human genome build 37, and if not is it possible to change to 37? Thanks again   ...
written 18 months ago by anitabaery0
0
votes
1
answer
606
views
1
answers
Comment: C: Clariom D Assays, annotation
... Thank you for that James. So, I run according to your suggestions, but the output doesn't look right: fd$CHR <- mapIds(Homo.sapiens, as.character(fd$ENTREZID), "CDSCHROM", "ENTREZID") 'select()' returned 1:many mapping between keys and columns fd$CHRLOC <- mapIds(Homo.sapiens, as.character( ...
written 18 months ago by anitabaery0
0
votes
1
answer
606
views
1
answers
Comment: C: Clariom D Assays, annotation
... Thank you James, yes you are right fd$CHR and fd$CHR  are list objects. What I did was to change anno into matrix, list into data.frame and try cbind but the number or rows do not much. matrix <- exprs(anno) df <- data.frame(matrix(unlist(fd$CHRLOC)) ) df2 <- data.frame(matrix(unlist(fd ...
written 18 months ago by anitabaery0
0
votes
1
answer
606
views
1
answers
Comment: C: Clariom D Assays, annotation
... Hi James, Thanks very much. I have run: data.rma <- oligo::rma(data) library(affycoretools) anno <- annotateEset(data.rma, pd.clariom.d.human) library(Homo.sapiens) fd <- fData(anno) fd$CHR <- mapIds(Homo.sapiens, as.character(fd$ENTREZID), "CDSCHROM", "ENTREZID") fd$CHRLOC <- ...
written 18 months ago by anitabaery0
0
votes
1
answer
606
views
1
answers
Comment: C: Clariom D Assays, annotation
... Hi James. Thank you for your reply. Yes, you are right "write" didn't work properly, using data.frame did. but in my annotated file I have the following columns: "PROBEID" "ID" "SYMBOL" "GENENAME" "Xsample1" "Xsample2" (...) 1. I do not know why "X" is added at the beginning of all my sample nam ...
written 18 months ago by anitabaery0
0
votes
1
answer
606
views
1
answer
Clariom D Assays, annotation
... Hi, I am using Clariom D Assays arrays and have tried to annotate it using the following: library(oligo) rma <- oligo::rma(data) library(affycoretools) anno<- annotateEset(rma, pd.clariom.d.human) write.table(anno, file = "anno.txt") Unfortunately, I got not annotated txt file with samp ...
annotation written 18 months ago by anitabaery0 • updated 18 months ago by James W. MacDonald50k

Latest awards to anitabaery

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 153 users visited in the last hour