User: salamandra

gravatar for salamandra
salamandra350
Reputation:
350
Status:
Trusted
Location:
Last seen:
4 months, 2 weeks ago
Joined:
5 years, 6 months ago
Email:
t*************@gmail.com

Posts by salamandra

<prev • 224 results • page 1 of 23 • next >
0
votes
1
answer
254
views
1
answers
Comment: C: Affymetrix: probeset or transcript cluster?
... ah ok, I was doing wrong. thank you! ...
written 4 months ago by salamandra350
0
votes
1
answer
254
views
1
answers
Comment: C: Affymetrix: probeset or transcript cluster?
... Doing the way you say for 1st example gives only 215 successfully converted ids of a total of 33297 ...
written 4 months ago by salamandra350
0
votes
1
answer
254
views
1
answers
Comment: C: Affymetrix: probeset or transcript cluster?
... thank you for answering, but meanwhile I tested how many ids were converted successfully in both probeset and transcriptcluster with: sum(!is.na(resultTable$ENSEMBL)) 1st example - GSE75918: *hugene10stprobeset.db*: 327424 ids; *hugene10sttranscriptcluster.db*: 215 ids 2nd example - GSE63296: ...
written 4 months ago by salamandra350
0
votes
1
answer
254
views
1
answers
Comment: C: Affymetrix: probeset or transcript cluster?
... I am doing this for studies on GEO, so the array platform varies. Examples: [GSE75918][1] study. the array platform is [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]. it works with both transcriptcluster and probeset., but with both there are many NAs. eg of ids: "7 ...
written 4 months ago by salamandra350
5
votes
1
answer
254
views
1
answer
Affymetrix: probeset or transcript cluster?
... I used to first normalize Affymetrix microarray data with RMA by 'probeset': oligo::rma(rawData, background=TRUE, normalize=TRUE, target="probeset") and then convert probe ids to gene ids with: select(microarrayPackage, keys = as.character(ids), column = c('PROBEID','ENSEMBL'), keytype='P ...
R oligo microarray affymetrix written 4 months ago by salamandra350
2
votes
1
answer
210
views
1
answer
Summarize by gene for agilent microarray data - one color
... I want to normalize agilent data (one color array). Followed limma package user guide, but in the end got some genes repeated for different probes. How can I get data summarized by gene instead of probe? Is it ok, to just average probes of same gene? Code so far: library(limma) library(t ...
R microarray limma written 4 months ago by salamandra350 • updated 4 months ago by Kevin Blighe69k
0
votes
2
answers
1.1k
views
2
answers
Comment: C: Does Gene length corrected TMM [GeTMM] violate any assumptions of TMM normalizat
... I understand your point, but why then in the article they use GeTMM for DE as well? See figure 7 [here][1] [1]: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2246-7 ...
written 8 months ago by salamandra350
0
votes
0
answers
215
views
0
answers
Which annotation package to use to mapIds() on HuEx-1_0-st-v2 microarray platform?
... when running: microarrayPackage = 'pd.huex.1.0.st.v2' mapIds(eval(parse(text = microarrayPackage)), keys = ids, column = 'ENSEMBL', keytype='PROBEID') I get the error: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘mapIds’ for sign ...
R bioconductor microarray written 11 months ago by salamandra350
0
votes
1
answer
2.0k
views
1
answers
Comment: C: Human Exon array probeset to gene-level expression
... From GeneAnnot site we can see that different probe sets that target same gene have variable numbers of same probes. For example for gene MAPK1 there is: [1552264_a_at probe set][1] has probes 1 to 11, while [224621_at probe set][2] has probes 1 to 3 and 8 to 11. For same probe set, different combin ...
written 14 months ago by salamandra350
0
votes
1
answer
2.0k
views
1
answers
Comment: C: Human Exon array probeset to gene-level expression
... If they are different isoforms, doing an average of two might not be appropriate cause one might no be expressed and that brings gene expression down.. ...
written 14 months ago by salamandra350

Latest awards to salamandra

Great Question 4 months ago, created a question with more than 5,000 views. For Export graph in R - error QuartzBitmap_Output - unable to open file
Popular Question 8 months ago, created a question with more than 1,000 views. For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Popular Question 8 months ago, created a question with more than 1,000 views. For Files to compare ChIP vs Input on genome browser: after alignment or peak calling?
Epic Question 8 months ago, created a question with more than 10,000 views. For Export graph in R - error QuartzBitmap_Output - unable to open file
Popular Question 8 months ago, created a question with more than 1,000 views. For Remove/Identify pseudogenes from a list of Entrez IDs programatically
Popular Question 8 months ago, created a question with more than 1,000 views. For Which peaks in the bed file output by MACS2 are significant ?
Popular Question 11 months ago, created a question with more than 1,000 views. For Files to compare ChIP vs Input on genome browser: after alignment or peak calling?
Popular Question 11 months ago, created a question with more than 1,000 views. For What is chr EBV in human sam file?
Popular Question 11 months ago, created a question with more than 1,000 views. For Remove/Identify pseudogenes from a list of Entrez IDs programatically
Popular Question 11 months ago, created a question with more than 1,000 views. For Why command gives the error: extra operand 23243?
Popular Question 11 months ago, created a question with more than 1,000 views. For Enrichment heatmap - GOstats package of R
Popular Question 11 months ago, created a question with more than 1,000 views. For MACS for chip-seq: difference between sonication size(bandwidth) and fragment size?
Popular Question 11 months ago, created a question with more than 1,000 views. For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Popular Question 11 months ago, created a question with more than 1,000 views. For Does adapter removal (with trimmomatic) also remove barcodes?
Popular Question 14 months ago, created a question with more than 1,000 views. For Remove/Identify pseudogenes from a list of Entrez IDs programatically
Popular Question 14 months ago, created a question with more than 1,000 views. For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Popular Question 14 months ago, created a question with more than 1,000 views. For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Popular Question 14 months ago, created a question with more than 1,000 views. For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Popular Question 15 months ago, created a question with more than 1,000 views. For Remove/Identify deprecated IDs from a list of Entrez IDs programatically

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2041 users visited in the last hour
_