Hello,

I want to analyze entire Connectivity Map dataset (~120 drugs, ~560 arrays, two chipsets (HG-U133A and HTHG-U133A)). I am reading the series matrix file available on [GEO][1]. As I want the differential expression of group of instances where cell line is same, platform is same, drug and its concentration is same so to build classes to determine which replicate is in which particular condition I have to do something like this:

```r
data <- getGEO('GSE5258')
eset <- data[[2]] # Taking GPL96 array into an expression set
show(pData(phenoData(eset))[1:2,])

                   title geo_accession                status submission_date last_update_date type channel_count source_name_ch1 organism_ch1         characteristics_ch1 characteristics_ch1.1 characteristics_ch1.2
GSM118720 EC2003090503AA     GSM118720 Public on Sep 27 2006     Jul 06 2006      Sep 18 2006  RNA             1     cmap_well:3 Homo sapiens perturbagen: small molecule       type: treatment       name: metformin
GSM118721 EC2003090502AA     GSM118721 Public on Sep 27 2006     Jul 06 2006      Sep 18 2006  RNA             1     cmap_well:2 Homo sapiens perturbagen: small molecule         type: control            name: null
            characteristics_ch1.3 characteristics_ch1.4 characteristics_ch1.5 characteristics_ch1.6 characteristics_ch1.7 molecule_ch1 label_ch1 taxid_ch1                                    description data_processing platform_id
GSM118720 concentration: .00001 M       vehicle: medium   vehicle_final: null         duration: 6 h            cell: MCF7    total RNA    biotin      9606 MCF7 treated with metformin (.00001 M) for 6 h         MAS 5.0       GPL96
GSM118721     concentration: null       vehicle: medium   vehicle_final: null         duration: 6 h            cell: MCF7    total RNA    biotin      9606             MCF7 with vehicle (medium) for 6 h         MAS 5.0       GPL96

h1=as.numeric(pData(eset)["characteristics_ch1.2"]=="name: metformin") # In a logical operator (h1) put 1 where drug = metformin and 0 otherwise and it works fine.

h1

[1] 1 0 1 1 1 0 0 0 0 1 0 0 ...... [346] 0
```

Now I want to apply multiple conditions: where `drug == "metformin"` AND `cell line == "MCF7"`

```r
c1=as.numeric(pData(eset)$characteristics_ch1.2=="name: metformin" && characteristics_ch1.7=="cell: MCF7")
Error: object 'characteristics_ch1.7' not found
```

I am unable to apply multiple conditions here. I am even not sure if the approach I am following will work as well. Kindly share your views about the problem. Thank you.

 [1]: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5258
```r
c1=as.numeric(pData(eset)$characteristics_ch1.2=="name: metformin" && pData(eset)$characteristics_ch1.7=="cell: MCF7")
```

The error message was very informative in this case.