User: Srinivas Iyyer

gravatar for Srinivas Iyyer
Reputation:
590
Status:
Trusted
Location:
Last seen:
10 years, 10 months ago
Joined:
15 years, 2 months ago
Email:
s**************@yahoo.com

Posts by Srinivas Iyyer

<prev • 58 results • page 1 of 6 • next >
0
votes
1
answer
1.1k
views
1
answer
Creating Affymetrix CDF files
... Hello: What is a CDF file and what should be the contents of it (format) and how should I make it. My question is: I have a probe, its coordinates and annotation in tab delim file. Prob X cord Prob Y cord type (PM) pbset name annotations I have this for u95av2. Now I want to run RMA on on ...
annotation cdf probe written 10.9 years ago by Srinivas Iyyer590 • updated 10.9 years ago by Kasper Daniel Hansen6.4k
0
votes
1
answer
673
views
1
answer
ArrayExpress package error
... Dear Group, I have been trying to create rawset using ArrayExpress for the following array dataset. I have error when I ran the following. Any thoughts if error is with the compiled data or functions. thank you. srini (sessionInfo - given below) > rawset = ArrayExpress("E-SMDB-3834") trying URL ...
arrayexpress written 11.1 years ago by Srinivas Iyyer590 • updated 11.0 years ago by audrey280
0
votes
1
answer
454
views
1
answer
layout cDNA in limma
... Dear group, I downloaded raw data from UNC genome center. These are agilent ver 1 chips (from Chuck Perou's lab). (GSE686). looking at header they appear to be smd.old format. (header names given below as comma sep). when I read RG file: RG <- read.maimages(files,source="smd.old") > RG$ge ...
written 11.1 years ago by Srinivas Iyyer590 • updated 11.1 years ago by Sean Davis21k
0
votes
2
answers
909
views
2
answers
Comment: C: GEOQuery - MAS5 normalized data
... Sorry! I forgot to do attach the required information. > sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached ...
written 11.1 years ago by Srinivas Iyyer590
0
votes
2
answers
909
views
2
answers
GEOQuery - MAS5 normalized data
... Dear group / Dear Sean, I am using GEOQuery to download a MAS5 (U133Plus2 platform) and intend to make it into a expression matrix and compute differential expression between two classes of samples. I have downloaded the data into a gse object. while making a exprSet object using code in vignette: ...
geoquery written 11.1 years ago by Srinivas Iyyer590 • updated 11.1 years ago by Francois Pepin1.3k
0
votes
0
answers
433
views
0
answers
sigPathway on Agilent data
... Dear group, How can I do sigPathway analysis for an agilent experiment. My experimental design: I have 10 chips data. Chips are hybridized by normal and treated from same mouse. sigpathway requires a phenotype label file: indicating 0 (say normal) and 1 (disease). In case of my experiment (two c ...
sigpathway written 11.5 years ago by Srinivas Iyyer590
0
votes
2
answers
764
views
2
answers
Comment: C: making gene sets for geneSetTest of Limma
... Dear Martin, Thank you for your email. I should have explained straight and simple. I want to associate my differentially expressed genes ( data from lmfit and ebayes) to 10 different gene expression studies. What i have from those 10 studies is list of genes that are differentially expressed. Iv ...
written 11.5 years ago by Srinivas Iyyer590
0
votes
2
answers
764
views
2
answers
making gene sets for geneSetTest of Limma
... Dear group, i want to convert all gene sets available from GSEA (C1,C2,C3 and C4) into a 4 different gene sets, so that I can use geneSetTest of limma on above 4 different gene sets. In one of the examples (classic estrogen example, only one set is described). What kind of formats geneSetTest wil ...
limma convert written 11.5 years ago by Srinivas Iyyer590 • updated 11.5 years ago by Gordon Smyth39k
0
votes
1
answer
770
views
1
answer
obtaining genes responsible for over-representation of GO term - GOstats
... dear group, when i use GOstats, i get some terms as over represented for my set of genes. I am interested now in getting those specific genes responsible for enrichment of a term. How can i obtain those genes. more clearly, i have a set of differentially expressed genes, i did GOstats for obtaini ...
gostats written 11.6 years ago by Srinivas Iyyer590 • updated 11.6 years ago by James W. MacDonald52k
0
votes
1
answer
577
views
1
answer
Agilent spike-in probes
... Dear Naomi, How can I remove control probes before doing expression analysis. i am following some steps lile the followings. RG <- read.maimages(files$targes,'agilent') RG.b <- backgroundSubtraction(RG,method='normexp',offset=50) MA <- normalizewithinarrays(RG.b,method='loess'). Where ...
annotation normalization go hgug4112a limma written 11.7 years ago by Srinivas Iyyer590 • updated 11.7 years ago by Sean Davis21k

Latest awards to Srinivas Iyyer

Popular Question 10.9 years ago, created a question with more than 1,000 views. For Limma - Gene set test
Popular Question 10.9 years ago, created a question with more than 1,000 views. For How to get ENTREZID from Gene symbol in bioconductor
Popular Question 10.9 years ago, created a question with more than 1,000 views. For a question on creating model.matrix using limma
Popular Question 10.9 years ago, created a question with more than 1,000 views. For heatmap.2 coloring question
Popular Question 10.9 years ago, created a question with more than 1,000 views. For a question on creating model.matrix using limma

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 177 users visited in the last hour